Normalize count matrix

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=~condition)
#> converting counts to integer mode
head(counts(ids, norm=TRUE))
#>                       cc1       cc2       cc3       cc4       cc5       cc6
#> hsa-let-7a-2-3p  3.839715  4.957562  3.922234  4.193356  4.628304  4.320126
#> hsa-let-7a-3p    8.879606  9.912474  9.176849  8.724705  9.618618  8.956600
#> hsa-let-7a-5p   17.525920 18.324970 17.476047 17.414170 17.977366 17.531085
#> hsa-let-7b-3p    9.302412 11.360556  9.282137  9.880371 10.966974  9.778085
#> hsa-let-7b-5p   15.337173 16.405251 15.209072 15.416528 15.967481 15.401889
#> hsa-let-7c-3p    5.139584  5.142892  5.180718  5.353287  5.376405  5.413745
#>                       cc7       ct1       ct2       ct3       ct4       ct5
#> hsa-let-7a-2-3p  4.105222  2.962917  3.902602  3.760179  4.596888  4.575751
#> hsa-let-7a-3p    9.012317  9.240616  8.782452  8.762592  9.237904  9.168472
#> hsa-let-7a-5p   17.307877 18.861768 17.537454 17.523249 17.311227 17.382079
#> hsa-let-7b-3p   10.126883  9.621539  9.667149  9.273214 10.076857 10.090630
#> hsa-let-7b-5p   15.352952 15.631647 15.237137 15.078033 15.221224 15.242910
#> hsa-let-7c-3p    5.315111  4.270346  5.313367  5.600923  5.251170  5.149174
#>                       ct6       ct7
#> hsa-let-7a-2-3p  4.316038  3.852731
#> hsa-let-7a-3p    8.755662  9.090326
#> hsa-let-7a-5p   17.698660 17.638359
#> hsa-let-7b-3p   10.382668  9.999591
#> hsa-let-7b-5p   15.785968 15.537679
#> hsa-let-7c-3p    5.091561  4.953205