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

Description Usage Arguments

View source: R/CsawAnalysis.R

Description

Analyze bam files with csaw and produces corresponding graphs.

Usage

1
2
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 June 19, 2018, 8:26 p.m.