diff --git a/articles/docker.html b/articles/docker.html index cc99108..feb0953 100644 --- a/articles/docker.html +++ b/articles/docker.html @@ -89,7 +89,7 @@


-Vignette updated: Jun-26-2024
+Vignette updated: Jun-28-2024

Source: vignettes/docker.Rmd @@ -165,7 +165,7 @@

Session Info
 utils::sessionInfo()
-
## R version 4.4.0 (2024-04-24)
+
## R Under development (unstable) (2024-03-28 r86224)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -191,55 +191,59 @@ 
Session Info## [1] MotifPeeker_0.99.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] tidyselect_1.2.1            viridisLite_0.4.2          
-##  [3] dplyr_1.1.4                 blob_1.2.4                 
-##  [5] viridis_0.6.5               filelock_1.0.3             
-##  [7] Biostrings_2.73.1           bitops_1.0-7               
-##  [9] fastmap_1.2.0               lazyeval_0.2.2             
-## [11] BiocFileCache_2.13.0        GenomicAlignments_1.41.0   
-## [13] digest_0.6.35               lifecycle_1.0.4            
-## [15] RSQLite_2.3.7               magrittr_2.0.3             
-## [17] compiler_4.4.0              rlang_1.1.4                
-## [19] sass_0.4.9                  tools_4.4.0                
-## [21] utf8_1.2.4                  yaml_2.3.8                 
-## [23] data.table_1.15.4           knitr_1.47                 
-## [25] S4Arrays_1.5.1              htmlwidgets_1.6.4          
-## [27] bit_4.0.5                   curl_5.2.1                 
-## [29] DelayedArray_0.31.3         abind_1.4-5                
-## [31] BiocParallel_1.39.0         purrr_1.0.2                
-## [33] BiocGenerics_0.51.0         desc_1.4.3                 
-## [35] grid_4.4.0                  stats4_4.4.0               
-## [37] fansi_1.0.6                 colorspace_2.1-0           
-## [39] ggplot2_3.5.1               MASS_7.3-60.2              
-## [41] scales_1.3.0                SummarizedExperiment_1.35.0
-## [43] cli_3.6.2                   rmarkdown_2.27             
-## [45] crayon_1.5.2                ragg_1.3.2                 
-## [47] generics_0.1.3              emoji_15.0                 
-## [49] httr_1.4.7                  DBI_1.2.3                  
-## [51] cachem_1.1.0                stringr_1.5.1              
-## [53] zlibbioc_1.51.1             parallel_4.4.0             
-## [55] XVector_0.45.0              universalmotif_1.23.0      
-## [57] matrixStats_1.3.0           vctrs_0.6.5                
-## [59] Matrix_1.7-0                jsonlite_1.8.8             
-## [61] IRanges_2.39.0              S4Vectors_0.43.0           
-## [63] bit64_4.0.5                 systemfonts_1.1.0          
-## [65] plotly_4.10.4               tidyr_1.3.1                
-## [67] jquerylib_0.1.4             glue_1.7.0                 
-## [69] pkgdown_2.0.9               codetools_0.2-20           
-## [71] DT_0.33                     stringi_1.8.4              
-## [73] gtable_0.3.5                GenomeInfoDb_1.41.1        
-## [75] GenomicRanges_1.57.1        UCSC.utils_1.1.0           
-## [77] munsell_0.5.1               tibble_3.2.1               
-## [79] pillar_1.9.0                htmltools_0.5.8.1          
-## [81] GenomeInfoDbData_1.2.12     R6_2.5.1                   
-## [83] dbplyr_2.5.0                textshaping_0.4.0          
-## [85] evaluate_0.24.0             tidyverse_2.0.0            
-## [87] Biobase_2.65.0              lattice_0.22-6             
-## [89] Rsamtools_2.21.0            memoise_2.0.1              
-## [91] bslib_0.7.0                 Rcpp_1.0.12                
-## [93] gridExtra_2.3               SparseArray_1.5.10         
-## [95] xfun_0.44                   fs_1.6.4                   
-## [97] MatrixGenerics_1.17.0       pkgconfig_2.0.3

+##   [1] tidyselect_1.2.1            viridisLite_0.4.2          
+##   [3] dplyr_1.1.4                 blob_1.2.4                 
+##   [5] viridis_0.6.5               filelock_1.0.3             
+##   [7] Biostrings_2.73.1           bitops_1.0-7               
+##   [9] fastmap_1.2.0               lazyeval_0.2.2             
+##  [11] RCurl_1.98-1.14             BiocFileCache_2.13.0       
+##  [13] GenomicAlignments_1.41.0    XML_3.99-0.17              
+##  [15] digest_0.6.36               lifecycle_1.0.4            
+##  [17] RSQLite_2.3.7               magrittr_2.0.3             
+##  [19] compiler_4.5.0              rlang_1.1.4                
+##  [21] sass_0.4.9                  tools_4.5.0                
+##  [23] utf8_1.2.4                  yaml_2.3.8                 
+##  [25] data.table_1.15.4           rtracklayer_1.65.0         
+##  [27] knitr_1.47                  S4Arrays_1.5.1             
+##  [29] htmlwidgets_1.6.4           bit_4.0.5                  
+##  [31] curl_5.2.1                  DelayedArray_0.31.3        
+##  [33] abind_1.4-5                 BiocParallel_1.39.0        
+##  [35] purrr_1.0.2                 BiocGenerics_0.51.0        
+##  [37] desc_1.4.3                  grid_4.5.0                 
+##  [39] stats4_4.5.0                fansi_1.0.6                
+##  [41] colorspace_2.1-0            ggplot2_3.5.1              
+##  [43] MASS_7.3-60.2               scales_1.3.0               
+##  [45] SummarizedExperiment_1.35.0 cli_3.6.3                  
+##  [47] rmarkdown_2.27              crayon_1.5.3               
+##  [49] ragg_1.3.0                  generics_0.1.3             
+##  [51] tzdb_0.4.0                  httr_1.4.7                 
+##  [53] rjson_0.2.21                DBI_1.2.3                  
+##  [55] cachem_1.1.0                ggseqlogo_0.2              
+##  [57] zlibbioc_1.51.1             parallel_4.5.0             
+##  [59] universalmotif_1.23.0       XVector_0.45.0             
+##  [61] restfulr_0.0.15             matrixStats_1.3.0          
+##  [63] vctrs_0.6.5                 Matrix_1.7-0               
+##  [65] jsonlite_1.8.8              hms_1.1.3                  
+##  [67] IRanges_2.39.0              S4Vectors_0.43.0           
+##  [69] bit64_4.0.5                 systemfonts_1.0.6          
+##  [71] plotly_4.10.4               tidyr_1.3.1                
+##  [73] jquerylib_0.1.4             glue_1.7.0                 
+##  [75] pkgdown_2.0.9               memes_1.12.0               
+##  [77] codetools_0.2-19            DT_0.33                    
+##  [79] gtable_0.3.5                GenomeInfoDb_1.41.1        
+##  [81] BiocIO_1.15.0               GenomicRanges_1.57.1       
+##  [83] UCSC.utils_1.1.0            munsell_0.5.1              
+##  [85] tibble_3.2.1                pillar_1.9.0               
+##  [87] htmltools_0.5.8.1           GenomeInfoDbData_1.2.12    
+##  [89] BSgenome_1.73.0             R6_2.5.1                   
+##  [91] dbplyr_2.5.0                textshaping_0.3.7          
+##  [93] evaluate_0.24.0             Biobase_2.65.0             
+##  [95] lattice_0.22-6              readr_2.1.5                
+##  [97] Rsamtools_2.21.0            memoise_2.0.1              
+##  [99] bslib_0.7.0                 Rcpp_1.0.12                
+## [101] gridExtra_2.3               SparseArray_1.5.10         
+## [103] xfun_0.45                   fs_1.6.4                   
+## [105] MatrixGenerics_1.17.0       pkgconfig_2.0.3


diff --git a/articles/templateR.html b/articles/templateR.html index ab0efd2..3e2527c 100644 --- a/articles/templateR.html +++ b/articles/templateR.html @@ -89,7 +89,7 @@


-Vignette updated: Jun-26-2024
+Vignette updated: Jun-28-2024

Source: vignettes/templateR.Rmd @@ -110,7 +110,7 @@

Session Info
 utils::sessionInfo()
-
## R version 4.4.0 (2024-04-24)
+
## R Under development (unstable) (2024-03-28 r86224)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -136,55 +136,59 @@ 
Session Info## [1] MotifPeeker_0.99.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] tidyselect_1.2.1            viridisLite_0.4.2          
-##  [3] dplyr_1.1.4                 blob_1.2.4                 
-##  [5] viridis_0.6.5               filelock_1.0.3             
-##  [7] Biostrings_2.73.1           bitops_1.0-7               
-##  [9] fastmap_1.2.0               lazyeval_0.2.2             
-## [11] BiocFileCache_2.13.0        GenomicAlignments_1.41.0   
-## [13] digest_0.6.35               lifecycle_1.0.4            
-## [15] RSQLite_2.3.7               magrittr_2.0.3             
-## [17] compiler_4.4.0              rlang_1.1.4                
-## [19] sass_0.4.9                  tools_4.4.0                
-## [21] utf8_1.2.4                  yaml_2.3.8                 
-## [23] data.table_1.15.4           knitr_1.47                 
-## [25] S4Arrays_1.5.1              htmlwidgets_1.6.4          
-## [27] bit_4.0.5                   curl_5.2.1                 
-## [29] DelayedArray_0.31.3         abind_1.4-5                
-## [31] BiocParallel_1.39.0         purrr_1.0.2                
-## [33] BiocGenerics_0.51.0         desc_1.4.3                 
-## [35] grid_4.4.0                  stats4_4.4.0               
-## [37] fansi_1.0.6                 colorspace_2.1-0           
-## [39] ggplot2_3.5.1               MASS_7.3-60.2              
-## [41] scales_1.3.0                SummarizedExperiment_1.35.0
-## [43] cli_3.6.2                   rmarkdown_2.27             
-## [45] crayon_1.5.2                ragg_1.3.2                 
-## [47] generics_0.1.3              emoji_15.0                 
-## [49] httr_1.4.7                  DBI_1.2.3                  
-## [51] cachem_1.1.0                stringr_1.5.1              
-## [53] zlibbioc_1.51.1             parallel_4.4.0             
-## [55] XVector_0.45.0              universalmotif_1.23.0      
-## [57] matrixStats_1.3.0           vctrs_0.6.5                
-## [59] Matrix_1.7-0                jsonlite_1.8.8             
-## [61] IRanges_2.39.0              S4Vectors_0.43.0           
-## [63] bit64_4.0.5                 systemfonts_1.1.0          
-## [65] plotly_4.10.4               tidyr_1.3.1                
-## [67] jquerylib_0.1.4             glue_1.7.0                 
-## [69] pkgdown_2.0.9               codetools_0.2-20           
-## [71] DT_0.33                     stringi_1.8.4              
-## [73] gtable_0.3.5                GenomeInfoDb_1.41.1        
-## [75] GenomicRanges_1.57.1        UCSC.utils_1.1.0           
-## [77] munsell_0.5.1               tibble_3.2.1               
-## [79] pillar_1.9.0                htmltools_0.5.8.1          
-## [81] GenomeInfoDbData_1.2.12     R6_2.5.1                   
-## [83] dbplyr_2.5.0                textshaping_0.4.0          
-## [85] evaluate_0.24.0             tidyverse_2.0.0            
-## [87] Biobase_2.65.0              lattice_0.22-6             
-## [89] Rsamtools_2.21.0            memoise_2.0.1              
-## [91] bslib_0.7.0                 Rcpp_1.0.12                
-## [93] gridExtra_2.3               SparseArray_1.5.10         
-## [95] xfun_0.44                   fs_1.6.4                   
-## [97] MatrixGenerics_1.17.0       pkgconfig_2.0.3

+##   [1] tidyselect_1.2.1            viridisLite_0.4.2          
+##   [3] dplyr_1.1.4                 blob_1.2.4                 
+##   [5] viridis_0.6.5               filelock_1.0.3             
+##   [7] Biostrings_2.73.1           bitops_1.0-7               
+##   [9] fastmap_1.2.0               lazyeval_0.2.2             
+##  [11] RCurl_1.98-1.14             BiocFileCache_2.13.0       
+##  [13] GenomicAlignments_1.41.0    XML_3.99-0.17              
+##  [15] digest_0.6.36               lifecycle_1.0.4            
+##  [17] RSQLite_2.3.7               magrittr_2.0.3             
+##  [19] compiler_4.5.0              rlang_1.1.4                
+##  [21] sass_0.4.9                  tools_4.5.0                
+##  [23] utf8_1.2.4                  yaml_2.3.8                 
+##  [25] data.table_1.15.4           rtracklayer_1.65.0         
+##  [27] knitr_1.47                  S4Arrays_1.5.1             
+##  [29] htmlwidgets_1.6.4           bit_4.0.5                  
+##  [31] curl_5.2.1                  DelayedArray_0.31.3        
+##  [33] abind_1.4-5                 BiocParallel_1.39.0        
+##  [35] purrr_1.0.2                 BiocGenerics_0.51.0        
+##  [37] desc_1.4.3                  grid_4.5.0                 
+##  [39] stats4_4.5.0                fansi_1.0.6                
+##  [41] colorspace_2.1-0            ggplot2_3.5.1              
+##  [43] MASS_7.3-60.2               scales_1.3.0               
+##  [45] SummarizedExperiment_1.35.0 cli_3.6.3                  
+##  [47] rmarkdown_2.27              crayon_1.5.3               
+##  [49] ragg_1.3.0                  generics_0.1.3             
+##  [51] tzdb_0.4.0                  httr_1.4.7                 
+##  [53] rjson_0.2.21                DBI_1.2.3                  
+##  [55] cachem_1.1.0                ggseqlogo_0.2              
+##  [57] zlibbioc_1.51.1             parallel_4.5.0             
+##  [59] universalmotif_1.23.0       XVector_0.45.0             
+##  [61] restfulr_0.0.15             matrixStats_1.3.0          
+##  [63] vctrs_0.6.5                 Matrix_1.7-0               
+##  [65] jsonlite_1.8.8              hms_1.1.3                  
+##  [67] IRanges_2.39.0              S4Vectors_0.43.0           
+##  [69] bit64_4.0.5                 systemfonts_1.0.6          
+##  [71] plotly_4.10.4               tidyr_1.3.1                
+##  [73] jquerylib_0.1.4             glue_1.7.0                 
+##  [75] pkgdown_2.0.9               memes_1.12.0               
+##  [77] codetools_0.2-19            DT_0.33                    
+##  [79] gtable_0.3.5                GenomeInfoDb_1.41.1        
+##  [81] BiocIO_1.15.0               GenomicRanges_1.57.1       
+##  [83] UCSC.utils_1.1.0            munsell_0.5.1              
+##  [85] tibble_3.2.1                pillar_1.9.0               
+##  [87] htmltools_0.5.8.1           GenomeInfoDbData_1.2.12    
+##  [89] BSgenome_1.73.0             R6_2.5.1                   
+##  [91] dbplyr_2.5.0                textshaping_0.3.7          
+##  [93] evaluate_0.24.0             Biobase_2.65.0             
+##  [95] lattice_0.22-6              readr_2.1.5                
+##  [97] Rsamtools_2.21.0            memoise_2.0.1              
+##  [99] bslib_0.7.0                 Rcpp_1.0.12                
+## [101] gridExtra_2.3               SparseArray_1.5.10         
+## [103] xfun_0.45                   fs_1.6.4                   
+## [105] MatrixGenerics_1.17.0       pkgconfig_2.0.3


diff --git a/index.html b/index.html index 714b9d0..19af4ba 100644 --- a/index.html +++ b/index.html @@ -85,7 +85,7 @@ Authors: Hiranyamaya Dash, Thomas Roberts, Nathan Skene

-Updated: Jun-26-2024 +Updated: Jun-28-2024

Introduction @@ -131,7 +131,7 @@

Session Info
 utils::sessionInfo()

-
## R version 4.4.0 (2024-04-24)
+
## R Under development (unstable) (2024-03-28 r86224)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -158,7 +158,7 @@ 
Session Info## 
 ## loaded via a namespace (and not attached):
 ##  [1] gtable_0.3.5        jsonlite_1.8.8      renv_1.0.7         
-##  [4] dplyr_1.1.4         compiler_4.4.0      BiocManager_1.30.23
+##  [4] dplyr_1.1.4         compiler_4.5.0      BiocManager_1.30.23
 ##  [7] tidyselect_1.2.1    rvcheck_0.2.1       scales_1.3.0       
 ## [10] yaml_2.3.8          fastmap_1.2.0       here_1.0.1         
 ## [13] ggplot2_3.5.1       R6_2.5.1            generics_0.1.3     
@@ -166,12 +166,12 @@ 
Session Info## [19] desc_1.4.3          dlstats_0.1.7       rprojroot_2.0.4    
 ## [22] munsell_0.5.1       pillar_1.9.0        RColorBrewer_1.1-3 
 ## [25] rlang_1.1.4         utf8_1.2.4          cachem_1.1.0       
-## [28] badger_0.2.4        xfun_0.44           fs_1.6.4           
-## [31] memoise_2.0.1       cli_3.6.2           magrittr_2.0.3     
-## [34] rworkflows_1.0.1    digest_0.6.35       grid_4.4.0         
+## [28] badger_0.2.4        xfun_0.45           fs_1.6.4           
+## [31] memoise_2.0.1       cli_3.6.3           magrittr_2.0.3     
+## [34] rworkflows_1.0.1    digest_0.6.36       grid_4.5.0         
 ## [37] lifecycle_1.0.4     vctrs_0.6.5         data.table_1.15.4  
 ## [40] evaluate_0.24.0     glue_1.7.0          fansi_1.0.6        
-## [43] colorspace_2.1-0    tools_4.4.0         pkgconfig_2.0.3    
+## [43] colorspace_2.1-0    tools_4.5.0         pkgconfig_2.0.3    
 ## [46] htmltools_0.5.8.1
diff --git a/pkgdown.yml b/pkgdown.yml index fa51411..c1dcf00 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,8 +1,8 @@ -pandoc: '3.2' +pandoc: 3.1.1 pkgdown: 2.0.9 pkgdown_sha: ~ articles: docker: docker.html templateR: templateR.html -last_built: 2024-06-26T15:02Z +last_built: 2024-06-28T17:53Z diff --git a/reference/MotifPeeker.html b/reference/MotifPeeker.html index 6549956..84465a2 100644 --- a/reference/MotifPeeker.html +++ b/reference/MotifPeeker.html @@ -87,11 +87,14 @@

Benchmark epigenomic profiling methods using motif enrichment

denovo_motif_discovery = TRUE, denovo_motifs = 3, motif_db = NULL, + trim_seq_width = NULL, download_buttons = TRUE, + meme_path = NULL, output_dir = tempdir(), + save_runfiles = FALSE, display = NULL, use_cache = TRUE, - ncpus = 1, + workers = 2, quiet = TRUE, debug = FALSE, verbose = FALSE @@ -185,17 +188,37 @@

Arguments

database has fewer than 50 entries.

+
trim_seq_width
+

An integer specifying the width of the sequence to +extract around the summit (default = NULL). This sequence is used to search +for de novo motifs. If not provided, the entire peak region will be used. +This parameter is intended to reduce the search space and speed up motif +discovery; therefore, a value less than the average peak width is +recommended. Peaks are trimmed symmetrically around the summit while +respecting the peak bounds.

+ +
download_buttons

A logical indicating whether to include download buttons for various files within the HTML report. (default = TRUE)

+
meme_path
+

path to meme/bin/ (optional). Defaut: NULL, searches +"MEME_PATH" environment variable or "meme_path" option for path to "meme/bin/".

+ +
output_dir

A character string specifying the directory to save the output files. (default = tempdir()) A sub-directory with the output files will be created in this directory.

+
save_runfiles
+

A logical indicating whether to save intermediate files +generated during the run, such as those from FIMO and AME. (default = FALSE)

+ +
display

A character vector specifying the display mode for the HTML report once it is generated. (default = NULL) Options are:

  • "browser": Open the report in the default web browser.

    • @@ -209,9 +232,8 @@

    Arguments

    previous runs. (default = TRUE)

-
ncpus
-

An integer specifying the number of cores to use for parallel -processing. (default = 1)

+
workers
+

The number of workers to use for parallel processing.

quiet
@@ -245,7 +267,8 @@

Details

Note

Running de-novo motif discovery is computationally expensive and can require from minutes to hours. denovo_motifs can widely affect the -runtime (higher values take longer).

+runtime (higher values take longer). Setting trim_seq_width to a lower +value can also reduce the runtime significantly.

@@ -287,12 +310,12 @@

Examples

download_buttons = TRUE, output_dir = tempdir(), use_cache = TRUE, - ncpus = 2, + workers = 2, debug = FALSE, quiet = TRUE, verbose = FALSE ) -#> [1] "/tmp/RtmpTLPcHi/MotifPeeker_20240626_150302" +#> [1] "/tmp/RtmpByXrE4/MotifPeeker_20240628_175311"
diff --git a/reference/bpapply.html b/reference/bpapply.html new file mode 100644 index 0000000..046e24f --- /dev/null +++ b/reference/bpapply.html @@ -0,0 +1,219 @@ + +Use BiocParallel functions with appropriate parameters — bpapply • MotifPeeker + + +
+
+ + + +
+
+
+

Use BiocParallel functions with appropriate parameters

+ Source: R/bpapply.R + +
+ +
+

Light wrapper around BiocParallel functions that +automatically sets the appropriate parameters based on the number of workers +specified.

+
+ +
+ 
bpapply(
+  X,
+  FUN,
+  apply_fun = BiocParallel::bplapply,
+  workers = 1,
+  progressbar = FALSE,
+  force_snowparam = FALSE,
+  verbose = FALSE,
+  ...
+)
+
+ +
+

Arguments

+
X
+

Any object for which methods length, [, and + [[ are implemented.

+ + +
FUN
+

The function to be applied to each element of X.

+ + +
apply_fun
+

A BiocParallel function to use +for parallel processing. (default = BiocParallel::bplapply)

+ + +
workers
+

The number of workers to use for parallel processing.

+ + +
progressbar
+

logical(1) Enable progress bar (based on plyr:::progress_text).

+ + +
force_snowparam
+

A logical indicating whether to force the use of +SnowParam object.

+ + +
verbose
+

A logical indicating whether to print verbose messages while +running the function. (default = FALSE)

+ + +
...
+

Arguments passed on to BiocParallel::bplapply, BiocParallel::bpmapply

BPPARAM
+

An optional BiocParallelParam instance + determining the parallel back-end to be used during evaluation, or a + list of BiocParallelParam instances, to be applied in + sequence for nested calls to BiocParallel functions.

+ +
BPREDO
+

A list of output from bplapply with one or + more failed elements. When a list is given in BPREDO, + bpok is used to identify errors, tasks are rerun and inserted + into the original results.

+ +
BPOPTIONS
+

Additional options to control the behavior of the parallel evaluation, see bpoptions.

+ +
MoreArgs
+

List of additional arguments to FUN.

+ +
SIMPLIFY
+

If TRUE the result will be simplified using + simplify2array.

+ +
USE.NAMES
+

If TRUE the result will be named.

+ + +
+ +
+
+

Value

+ + +

Output relevant to the apply_fun specified.

+
+ +
+

Examples

+ 
half_it <- function(arg1) return(arg1 / 2)
+x <- seq_len(10)
+
+res <- bpapply(x, half_it, workers = 2)
+print(res)
+#> [[1]]
+#> [1] 0.5
+#> 
+#> [[2]]
+#> [1] 1
+#> 
+#> [[3]]
+#> [1] 1.5
+#> 
+#> [[4]]
+#> [1] 2
+#> 
+#> [[5]]
+#> [1] 2.5
+#> 
+#> [[6]]
+#> [1] 3
+#> 
+#> [[7]]
+#> [1] 3.5
+#> 
+#> [[8]]
+#> [1] 4
+#> 
+#> [[9]]
+#> [1] 4.5
+#> 
+#> [[10]]
+#> [1] 5
+#> 
+
+
+
+
+ +
+ + +
+ + + + + + + + diff --git a/reference/check_ENCODE.html b/reference/check_ENCODE.html index fb9da65..7761fff 100644 --- a/reference/check_ENCODE.html +++ b/reference/check_ENCODE.html @@ -98,9 +98,12 @@

Value

Examples

- 
check_ENCODE("ENCFF109VAD", expect_format = "bam")
-#>                                                              BFC2 
-#> "/github/home/.cache/R/BiocFileCache/bf341948dfe_ENCFF109VAD.bam" 
+    
if (requireNamespace("curl", quietly = TRUE) &&
+    requireNamespace("jsonlite", quietly = TRUE)) {
+    check_ENCODE("ENCFF109VAD", expect_format = "bam")
+}
+#>                                                               BFC2 
+#> "/github/home/.cache/R/BiocFileCache/31184851a2e6_ENCFF109VAD.bam"
diff --git a/reference/check_JASPAR.html b/reference/check_JASPAR.html index 91f33cd..df7c35d 100644 --- a/reference/check_JASPAR.html +++ b/reference/check_JASPAR.html @@ -93,8 +93,8 @@

Value

Examples

check_JASPAR("MA1930.2")
-#>                                                              BFC3 
-#> "/github/home/.cache/R/BiocFileCache/bf32d5f43e1_MA1930.2.jaspar" 
+#>                                                               BFC3 
+#> "/github/home/.cache/R/BiocFileCache/31181ef1dbee_MA1930.2.jaspar"
diff --git a/reference/confirm_meme_install.html b/reference/confirm_meme_install.html new file mode 100644 index 0000000..4d88cdb --- /dev/null +++ b/reference/confirm_meme_install.html @@ -0,0 +1,113 @@ + +Stop if MEME suite is not installed — confirm_meme_install • MotifPeeker + + +
+
+ + + +
+
+
+

Stop if MEME suite is not installed

+ Source: R/confirm_meme_install.R + +
+ +
+

Stop if MEME suite is not installed

+
+ +
+ 
confirm_meme_install(meme_path = NULL)
+
+ +
+

Arguments

+
meme_path
+

path to meme/bin/ (optional). Defaut: NULL, searches +"MEME_PATH" environment variable or "meme_path" option for path to "meme/bin/".

+ +
+
+

Value

+ + +

Null

+
+
+

See also

+

check_meme_install

+
+ +
+ +
+ + +
+

Developed by Hiranyamaya Dash, Thomas Roberts, Nathan Skene.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
+ + + + + + + + diff --git a/reference/get_JASPARCORE.html b/reference/get_JASPARCORE.html index 747360c..bff0735 100644 --- a/reference/get_JASPARCORE.html +++ b/reference/get_JASPARCORE.html @@ -89,8 +89,8 @@

Value

Examples

get_JASPARCORE()
-#>                                                                                          BFC1 
-#> "/github/home/.cache/R/BiocFileCache/bf3548b1acf_JASPAR2024_CORE_non-redundant_pfms_meme.txt" 
+#>                                                                                           BFC1 
+#> "/github/home/.cache/R/BiocFileCache/31182cb22f18_JASPAR2024_CORE_non-redundant_pfms_meme.txt"
diff --git a/reference/get_bpparam.html b/reference/get_bpparam.html new file mode 100644 index 0000000..0cc0fe7 --- /dev/null +++ b/reference/get_bpparam.html @@ -0,0 +1,141 @@ + +Get parameters for BiocParallel — get_bpparam • MotifPeeker + + +
+
+ + + +
+
+
+

Get parameters for BiocParallel

+ Source: R/get_bpparam.R + +
+ +
+

Get appropriate parameters for BiocParallel based on the +number of workers specified. For less than 10 workers, the function returns a +MulticoreParam object. For 10 or more cores, the function +returns a SnowParam object. Since Windows supports +neither, the function returns a SerialParam object. As a +result, Windows users do not benefit from parallel processing.

+
+ +
+ 
get_bpparam(
+  workers,
+  progressbar = workers > 1,
+  force_snowparam = FALSE,
+  verbose = FALSE
+)
+
+ +
+

Arguments

+
workers
+

The number of workers to use for parallel processing.

+ + +
progressbar
+

logical(1) Enable progress bar (based on plyr:::progress_text).

+ + +
force_snowparam
+

A logical indicating whether to force the use of +SnowParam object.

+ + +
verbose
+

A logical indicating whether to print verbose messages while +running the function. (default = FALSE)

+ +
+
+

Value

+ + +

A BPPARAM object.

+
+
+

See also

+

BiocParallelParam

+
+ +
+ +
+ + +
+

Developed by Hiranyamaya Dash, Thomas Roberts, Nathan Skene.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
+ + + + + + + + diff --git a/reference/index.html b/reference/index.html index 1745d5c..45e30d4 100644 --- a/reference/index.html +++ b/reference/index.html @@ -75,6 +75,10 @@

All functions MotifPeeker()

Benchmark epigenomic profiling methods using motif enrichment

+ +

bpapply()

+ +

Use BiocParallel functions with appropriate parameters

calc_frip()

@@ -107,6 +111,10 @@

All functions motif_MA1930.2

Example CTCF JASPAR motif file

+ +

motif_enrichment()

+ +

Calculate motif enrichment in a set of sequences

read_motif_file()

@@ -123,10 +131,22 @@

All functions report_header()

Report header

+ +

segregate_seqs()

+ +

Segregate input sequences into common and unique groups

+ +

summit_to_motif()

+ +

Calculate the distance between peak summits and motifs

to_plotly()

Convert ggplot2 objects to plotly

+ +

trim_seqs()

+ +

Trim sequences to a specified width around the summit

+
+

See also

+

ggplotly

+

Examples

x <- data.frame(a = c(1,2,3), b = c(2,3,4))
 p <- ggplot2::ggplot(x, ggplot2::aes(x = a, y = b)) + ggplot2::geom_point()
 to_plotly(p, html_tags = FALSE)
-

-
+

+
diff --git a/reference/trim_seqs.html b/reference/trim_seqs.html new file mode 100644 index 0000000..f85c4e1 --- /dev/null +++ b/reference/trim_seqs.html @@ -0,0 +1,140 @@ + +Trim sequences to a specified width around the summit — trim_seqs • MotifPeeker + + +
+
+ + + +
+
+
+

Trim sequences to a specified width around the summit

+ Source: R/trim_seqs.R + +
+ +
+

Trim sequences to a specified width around the summit

+
+ +
+ 
trim_seqs(peaks, peak_width, genome_build, respect_bounds = TRUE)
+
+ +
+

Arguments

+
peaks
+

A GRanges object created using +read_peak_file().

+ + +
peak_width
+

Total expected width of the peak.

+ + +
genome_build
+

The genome build that the peak sequences should be +derived from.

+ + +
respect_bounds
+

Logical indicating whether the peak width should be +respected when trimming sequences. (default = TRUE) If TRUE, the +trimmed sequences will not extend beyond the peak boundaries.

+ +
+
+

Value

+ + +

A GRanges object with the trimmed sequences. The sequences are +guaranteed to not exceed the peak width + 1 (peak width + the summit +base).

+
+ +
+

Examples

+ 
data("CTCF_TIP_peaks", package = "MotifPeeker")
+peaks <- CTCF_TIP_peaks
+genome_build <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
+
+trimmed_seqs <- trim_seqs(peaks, peak_width = 100,
+                         genome_build = genome_build)
+summary(GenomicRanges::width(trimmed_seqs))
+#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
+#>    59.0   101.0   101.0    98.5   101.0   101.0 
+
+
+
+
+ +
+ + +
+

Developed by Hiranyamaya Dash, Thomas Roberts, Nathan Skene.

+
+ +
+

Site built with pkgdown 2.0.9.

+
+ +
+ + + + + + + + diff --git a/sitemap.xml b/sitemap.xml index 5fbac14..5c773db 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -33,6 +33,9 @@ /reference/MotifPeeker.html + + /reference/bpapply.html + /reference/calc_frip.html @@ -48,18 +51,27 @@ /reference/check_genome_build.html + + /reference/confirm_meme_install.html + /reference/format_exptype.html /reference/get_JASPARCORE.html + + /reference/get_bpparam.html + /reference/index.html /reference/link_JASPAR.html + + /reference/markov_background_model.html + /reference/messager.html @@ -69,9 +81,18 @@ /reference/motif_MA1930.2.html + + /reference/motif_enrichment.html + + + /reference/pipe.html + /reference/print_DT.html + + /reference/random_string.html + /reference/read_motif_file.html @@ -90,12 +111,21 @@ /reference/report_header.html + + /reference/segregate_seqs.html + /reference/stopper.html + + /reference/summit_to_motif.html + /reference/to_plotly.html + + /reference/trim_seqs.html + /reference/use_cache.html