This function normalizes raw count matrix using DESeq2::rlog() function from DESeq2::DESeq2-package.

isoNorm(ids, formula = NULL, maxSamples = 50)

Arguments

ids

Object of class IsomirDataSeq.

formula

Formula that will be used for normalization.

maxSamples

Maximum number of samples to use with DESeq2::rlog(), if not limma::voom() is used.

Value

IsomirDataSeq object with the normalized count matrix in a slot. The normalized matrix can be access with counts(ids, norm=TRUE).

Examples

data(mirData) ids <- isoCounts(mirData, minc=10, mins=6) ids <- isoNorm(mirData, formula=~group)
#> converting counts to integer mode
head(counts(ids, norm=TRUE))
#> cc1 cc2 cc3 ct2 ct3 ct4 #> hsa-let-7a-2-3p 2.535 3.112 2.576 2.563 2.523 2.899 #> hsa-let-7a-3p 9.013 9.725 9.213 8.939 8.957 9.231 #> hsa-let-7a-5p 17.644 18.203 17.619 17.639 17.662 17.490 #> hsa-let-7b-3p 9.558 10.978 9.553 9.778 9.559 10.044 #> hsa-let-7b-5p 15.452 16.198 15.376 15.374 15.304 15.361 #> hsa-let-7c-3p 4.628 4.646 4.658 4.726 4.921 4.686