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dev_strand_tests.R
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library(GenomicRanges)
library(ssvTracks)
options(mc.cores = 10)
pkg_dir = system.file(package = "ssvTracks", "extdata", mustWork = TRUE)
bam_files_runx1 = dir(pkg_dir, pattern = "RUNX1_RNA.+bam$", full.names = TRUE)
names(bam_files_runx1) = sub("_rep.+", "", basename(bam_files_runx1))
bed_file_runx1 = dir(pkg_dir, pattern = "RUNX1.bed", full.names = TRUE)
query_gr = rtracklayer::import.bed(bed_file_runx1)
strand(query_gr) = "-"
strand(query_gr) = "+"
cfg_dt = data.table(file = bam_files_runx1, name = names(bam_files_runx1))
track_rna.PE(cfg_dt,
query_gr,
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "strand", facet_VAR = "name", target_strand = "both")
track_rna.PE(cfg_dt,
GRanges("chr21", IRanges(34850e3, 34885e3)),
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "strand", facet_VAR = "name", target_strand = "both")
track_rna.PE(cfg_dt,
GRanges("chr21", IRanges(34859.4e3, 34859.6e3)),
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "strand", facet_VAR = "name", target_strand = "both")
track_rna.PE(cfg_dt,
query_gr,
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "name", facet_VAR = "strand", target_strand = "both")
track_rna.PE(cfg_dt,
query_gr,
show_splice = TRUE,
flip_strand = FALSE, fill_VAR = NULL, color_VAR = "strand", facet_VAR = "name", target_strand = "both")
track_rna.PE(cfg_dt,
query_gr,
show_splice = TRUE,
flip_strand = FALSE, fill_VAR = NULL, color_VAR = "strand", facet_VAR = "name")
track_rna.PE(cfg_dt,
query_gr,
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "strand", facet_VAR = "name")
pkg_dir = system.file(package = "ssvTracks", "extdata", mustWork = TRUE)
bam_files_esr1 = dir(pkg_dir, pattern = "M.+R1.ESR1_RNA.+bam$", full.names = TRUE)
names(bam_files_esr1) = sub("_R.+", "", basename(bam_files_esr1))
bed_file_esr1 = dir(pkg_dir, pattern = "ESR1.bed", full.names = TRUE)
query_gr = rtracklayer::import.bed(bed_file_esr1)
strand(query_gr) = "-"
strand(query_gr) = "+"
cfg_dt = data.table(file = bam_files_esr1, name = names(bam_files_esr1))
track_rna.SE(cfg_dt,
query_gr,
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "strand", facet_VAR = "name", target_strand = "both")
track_rna.SE(cfg_dt,
query_gr,
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "name", facet_VAR = "strand", target_strand = "both")
track_rna.SE(cfg_dt,
GRanges("chr6", IRanges(151800e3, 151850e3)),
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "name", facet_VAR = "strand", target_strand = "both")
track_rna.SE(cfg_dt,
GRanges("chr6", IRanges(151807e3, 151809e3)),
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "name", facet_VAR = "strand", target_strand = "both")
track_rna.SE(cfg_dt,
GRanges("chr6", IRanges(151807e3, 151809e3)),
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "name", facet_VAR = "strand", target_strand = "+")
#
track_rna.SE(cfg_dt,
GRanges("chr6", IRanges(151807e3, 151809e3)),
show_pileup = FALSE,
show_splice = TRUE, splice_within_range_only = GRanges("chr6", IRanges(151807e3, 151809e3)),
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "name", facet_VAR = "strand", target_strand = "+")
track_rna.SE(cfg_dt,
GRanges("chr6", IRanges(151807e3, 151809e3)),
show_pileup = FALSE,
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = "name", color_VAR = "name", facet_VAR = "name", target_strand = "+")
track_rna.SE(cfg_dt,
GRanges("chr6", IRanges(151807e3, 151809e3)),
show_splice = TRUE,
flip_strand = TRUE, fill_VAR = NULL, color_VAR = "name", facet_VAR = "strand", target_strand = "-")