REDseq (version 1.18.0)

summarizeByRE: Output count/weight summary by restriction enzyme cut site ID (REid)

Description

Output count/weight summary by REid with each row representing each REid

Usage

summarizeByRE(assignedSeqs, by=c("Weight", "REid"),sampleName="",round=TRUE)

Arguments

assignedSeqs

output from assignSeq2REsite

by

Weight if sum up the weight for each REid, REid if sum the occurrence of each REid.

sampleName

The name of the sample used as the count column name.

round

TRUE: the sum of the weight is rounded up if the fraction part is greater than 0.5. FALSE: as it is.

Value

a matrix with REid as the first column and total count/weight as the second column, that can be used for the downstream analysis with DEseq or edgeR.

See Also

summarizeBySeq, assignSeq2REsite

Examples

	library(REDseq)
	data(example.assignedREDseq)
	summarizeByRE(example.assignedREDseq,by="REid",sampleName="example")
	summarizeByRE(example.assignedREDseq,by="Weight",sampleName="example")