PlotDistr: This function generates CPMW distribtion curve and barplot...

In stjude/ChIPseqSpikeInFree: A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications

This function generates CPMW distribtion curve and barplot using sacaling factor table.

Description

This function generates CPMW distribtion curve and barplot using sacaling factor table.

Usage

PlotDistr(data, SF = "test_SF.txt", prefix = "test", xlimMaxCPMW = NULL)

Arguments

data	a data.frame generated by function ParseReadCounts() or a file name of parsed matrix
prefix	prefix of output filename to save the plots and scaling factor values.
xlimMaxCPMW	NULL or a numeric value [ between 10 and 100 ] to define maximum CPMW in the distribtion plot (xlim).
metaFile	a data.frame of metadata by ReadMeta(); or a filename of metadata file.

Value

None

Examples

## 1. start from a parsedMatrix file

# parsedMatrixFile <- "your/path/test_parsedMatrix.txt"
# metaFile <- "your/path/sample_meta.txt"
# parsedDF <- read.table(parsedMatrixFile, sep="\t",header=TRUE,fill=TRUE,
# quote="",row.names=NULL ,check.names=F)

## use defalut setting 
# SF <- CalculateSF(data = parsedDF, metaFile = metaFile)  
# PlotDistr (data=parsedDF,SF=SF, prefix="your/path/test", xlimMaxCPMW=NULL)

## use custom setting for H3K9me3
# SF <- CalculateSF(data = parsedDF, metaFile = metaFile, 
#     maxLastTurn=0.97, cutoff_QC=1)  
# PlotDistr (data=parsedDF,SF=SF, prefix="your/path/test_manual_cutoff", xlimMaxCPMW=NULL)

## zoom out distribution curve
# PlotDistr (data=parsedDF,SF=SF, prefix="your/path/test_manual_cutoff_zoom", xlimMaxCPMW=50)

stjude/ChIPseqSpikeInFree documentation built on March 28, 2022, 5:36 a.m.