summarizeByRE {REDseq} | R Documentation |
Output count/weight summary by REid with each row representing each REid
summarizeByRE(assignedSeqs, by=c("Weight", "REid"),sampleName="",round=TRUE)
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. |
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.
Lihua Julie Zhu
summarizeBySeq, assignSeq2REsite
library(REDseq) data(example.assignedREDseq) summarizeByRE(example.assignedREDseq,by="REid",sampleName="example") summarizeByRE(example.assignedREDseq,by="Weight",sampleName="example")