Access counts matrix (avoid name clash with DESeq2::counts)

Access counts matrix (avoid name clash with DESeq2::counts)

Usage

getCounts(object)

Arguments

object

A geneda object

Value

Matrix or NULL

Examples

data(Snail1KO)
counts <- as.matrix(Snail1KO$rawCounts)
counts <- counts[rowSums(counts >= 10) >= 3, ]
meta <- Snail1KO$metadata
rownames(meta) <- meta$Sample
norm <- log2(t(t(counts) / colSums(counts)) * 1e6 + 1)
obj <- GenEDA(normalized = norm, metadata = meta, counts = counts)
getCounts(obj)[1:5, ]
#>          ERR1736465 ERR1736466 ERR1736467 ERR1736468 ERR1736469 ERR1736470
#> TSPAN6          434        829        334        779        578        602
#> DPM1           2202       3461       1627       4241       3676       3946
#> SCYL3            45         72         31        119         69         92
#> C1orf112        320        558        235        516        468        417
#> FUCA2          1987       3071       1599       3645       3121       3206