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89 gsora and gsea. #92
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2616875
initial getPatternGeneSet
jmitchell81 1485a94
initial GSEA
jmitchell81 7b76947
params for internal patternMarkers call
jmitchell81 ad8b720
"padj" replacing "q-value"
jmitchell81 8d53ccc
"PatternHallmark" to "PatternGeneSet"
jmitchell81 abe2da8
fct_order gene sets by significance
jmitchell81 3bd8379
pattern amplitude as enrichment stat
jmitchell81 bac3fc6
gene set names from list argument names
jmitchell81 ad2c512
specify function calls from dplyr, fgsea, forcats
jmitchell81 2459bb2
unit tests for getPatternGenSet
jmitchell81 b177189
specify padj threshold for geneset plot
jmitchell81 604b92f
trim comments
jmitchell81 0c80e32
use stored GIST result to test getPatternGeneSet
jmitchell81 f4d6237
getPatternGeneSet Generic
jmitchell81 b42ec49
remove getPatternHallmarks definition
jmitchell81 b4f17d3
testthat::expect_error for getPatternGeneSet
jmitchell81 770f3ef
update get and plot GeneSet generics
jmitchell81 0db9f33
devtools document update
jmitchell81 ccf59fa
switch to expect_no_error
jmitchell81 6aa129f
static hline threshold
jmitchell81 3bfe7d1
title specific to test method used
jmitchell81 a83199a
tests for plotPatternGeneSet
jmitchell81 6db63ed
remove object argument from plotPatternGeneSet
jmitchell81 2f6db07
remove object arguments from tests
jmitchell81 4ff7bf7
remove ggplot2::aes_string import
jmitchell81 6956f1e
replace getPatternGeneSet example in vignette
jmitchell81 5ca56ea
patternMarker parameters in getPatternGeneSet
jmitchell81 9a7ff3b
Remove documentation of object for plotting
jmitchell81 d69ee96
remove import biomart and msigdbr from DESC
jmitchell81 faa2ce5
load modsim data without filepath
jmitchell81 ceee671
remove second occurance of load()
jmitchell81 66e3955
Update DESCRIPTION
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17 changes: 10 additions & 7 deletions
17
man/plotPatternHallmarks-methods.Rd → man/plotPatternGeneSet-methods.Rd
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renaming needs to be done in also in
/vignettes/CoGAPs.rmd
to allow the package to build.stopping review here as the
R CMD build .
fails