csaw_analyze: Analyze bam files with csaw and produces corresponding...

In ArnaudDroitLab/ef.utils: Eric Utilities

Description

Analyze bam files with csaw and produces corresponding graphs.

Usage

csaw_analyze(correspondances, reference, genome.build,
  output.dir = "csaw_output/", threshold = 3, save.plots = TRUE)

Arguments

correspondances	A data frame with two columns: $Name Name (with the path) of the bam files. $Factors The factors to considerate during the analysis. Files with the same factor are replicas.
reference	The name of the reference factor.
genome.build	The name of the chosen annotation ("hg38", "hg19", "mm9", "mm10").
output.dir	The name of the directory where to save the files and graphs.
threshold	The threshold to consider while filtering data.
save.plots	Should plots and files created by csaw.save.plots be saved?

ArnaudDroitLab/ef.utils documentation built on Aug. 13, 2019, 9:09 p.m.