Man pages for kewiechecki/atacSeqFns
Utility functions for working with ATAC-seq peaks.

col.absColor scale for a specified quantile. This scale is intended...
col.zColor scale for a specified quantile. This scale is intended...
cond.colColor scale for categorical data.
cond.col.vecCreates a color scale for the levels in a vector, then...
CrobustaMotifsPWMs for 1487 potential TF binding sites.
dir.applyWrapper for applying a write function to each element of list...
dir.csvConcatenates a path, filename, and file extension into an...
dir.epsConcatenates a path, filename, and file extension into an...
dir.exportConcatenates a path, filename, and file extension into an...
dir.ggConcatenates a path, filename, and file extension into an...
dir.histAccepts a numeric vector and writes a histogram in EPS format...
dir.imgConcatenates a path, filename, and file extension into an...
dir.outConcatenates a path, filename, and file extension into an...
dir.pdfConcatenates a path, filename, and file extension into an...
dir.pngConcatenates a path, filename, and file extension into an...
dir.svgConcatenates a path, filename, and file extension into an...
dir.tabConcatenates a path, filename, and file extension into an...
getFeaturesParses a genome file in GFF format into a list of...
getMatchesSearches a given set of genomic ranges for the motifs...
getOverlapMatConverts gene-peak table to a logical matrix of associations
getOverlapsFinds all overlaps between one of the genomic features...
hm.annWrapper for 'hm.cell()' which applies cell dimensions to...
hm.cellWrapper for 'Heatmap()' which allows specifying cell...
hmdotaccepts the results of a hypergeometric test applied to each...
lrtabApplies a function to all file names in a specified directory...
matchPoisAccepts a vector of peak IDs, and performs a Poisson test for...
mkdateCreates a file path from a name, directory, and extension,...
regMatDetermines a matrix of potential regulatory TFs.
rmdupAccepts a PWMatrixList and an output from...
kewiechecki/atacSeqFns documentation built on Sept. 27, 2020, 8:25 a.m.