summarizeByRE: Output count/weight summary by restriction enzyme cut site ID...

In REDseq: Analysis of high-throughput sequencing data processed by restriction enzyme digestion

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.

Author(s)

Lihua Julie Zhu

See Also

summarizeBySeq, assignSeq2REsite

Examples

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

REDseq documentation built on Nov. 8, 2020, 8:19 p.m.