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))
#> pc2 pt2 pt7 pc1 pt6 pc3 pt3 pt5 pt4 #> hsa-let-7a-2-3p 11 7 10 13 4 13 9 3 0 #> hsa-let-7a-3p 928 745 1159 1293 613 973 1361 433 978 #> hsa-let-7a-5p 355578 324134 517950 507046 299028 375836 500423 152191 419754 #> hsa-let-7b-3p 1971 1410 1595 1646 1055 1267 1997 566 1148 #> hsa-let-7b-5p 77274 65928 92828 114643 53345 78586 96965 28974 71768 #> hsa-let-7c-3p 26 20 76 68 49 53 39 21 52 #> pc5 pc4 pc7 pc6 pt1 #> hsa-let-7a-2-3p 14 20 6 10 2 #> hsa-let-7a-3p 1614 1050 1219 637 542 #> hsa-let-7a-5p 468792 489195 340782 215635 150421 #> hsa-let-7b-3p 2852 1986 1724 875 760 #> hsa-let-7b-5p 93764 97902 68304 43050 29572 #> hsa-let-7c-3p 45 54 56 27 22