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.

Author

Lorena Pantano

Examples

data(mirData) head(counts(mirData))
#> cc1 cc2 cc3 cc4 cc5 cc6 cc7 ct1 ct2 #> hsa-let-7a-2-3p 5 13 4 9 11 6 7 0 4 #> hsa-let-7a-3p 767 707 630 609 731 389 681 258 496 #> hsa-let-7a-5p 317730 244832 203888 260931 244784 153049 220563 208511 222066 #> hsa-let-7b-3p 1037 1949 679 1385 1884 697 1499 338 931 #> hsa-let-7b-5p 69671 64702 42347 65322 60767 34975 56875 22215 45069 #> hsa-let-7c-3p 36 16 25 40 26 23 35 3 30 #> ct3 ct4 ct5 ct6 ct7 #> hsa-let-7a-2-3p 2 12 12 8 3 #> hsa-let-7a-3p 343 635 622 452 519 #> hsa-let-7a-5p 154246 175523 189733 230690 199923 #> hsa-let-7b-3p 494 1149 1194 1431 988 #> hsa-let-7b-5p 28312 41214 43058 61258 46600 #> hsa-let-7c-3p 28 26 24 22 17