The counts slot holds the count data as a matrix of non-negative integer count values, one row for each isomiR, and one column for each sample. The normalized matrix can be obtained by using the parameter norm=TRUE.

counts.IsomirDataSeq(object, norm = FALSE)

# S4 method for IsomirDataSeq
counts(object, norm = FALSE)

# S4 method for IsomirDataSeq,matrix
counts(object) <- value

Arguments

object

A IsomirDataSeq object.

norm

Boolean, return log2-normalized counts.

value

An integer matrix.

Value

base::matrix with raw or normalized count data.

Examples

data(mirData) head(counts(mirData))
#> cc1 cc2 cc3 ct2 ct3 ct4 #> hsa-let-7a-2-3p 5 13 4 4 2 12 #> hsa-let-7a-3p 767 707 630 496 343 635 #> hsa-let-7a-5p 317730 244832 203888 222066 154246 175523 #> hsa-let-7b-3p 1037 1949 679 931 494 1149 #> hsa-let-7b-5p 69671 64702 42347 45071 28312 41214 #> hsa-let-7c-3p 36 16 25 30 28 26