Melt Count Matrix to Long Format and log10 Transform

Melt Count Matrix to Long Format and log10 Transform

meltLog10(object, ...)

# S4 method for bcbioRNASeq
meltLog10(object, normalized = TRUE)

# S4 method for DESeqDataSet
meltLog10(object, normalized = TRUE)

# S4 method for DESeqTransform
meltLog10(object)

Arguments

object	Object.
...	Additional arguments (for the S4 generic definition).
normalized	Select normalized counts (TRUE), raw counts (FALSE), or specifically request TMM-normalized counts (tmm).

Value

log10 melted data.frame.

See also

reshape2::melt().

Examples

# bcbioRNASeq
meltLog10(bcb) %>% str()
#> 'data.frame':	922 obs. of  6 variables:
#>  $ ensgene    : chr  "ENSMUSG00000002459" "ENSMUSG00000004768" "ENSMUSG00000005886" "ENSMUSG00000016918" ...
#>  $ sampleID   : Factor w/ 4 levels "group1_1","group1_2",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ counts     : num  1.1206 2.6435 3.2752 2.8726 0.0414 ...
#>  $ sampleName : Factor w/ 4 levels "group1_1","group1_2",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ description: Factor w/ 4 levels "group1_1","group1_2",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ group      : Factor w/ 2 levels "ctrl","ko": 1 1 1 1 1 1 1 1 1 1 ...

# DESeqDataSet
meltLog10(dds) %>% str()
#> 'data.frame':	922 obs. of  7 variables:
#>  $ ensgene    : chr  "ENSMUSG00000002459" "ENSMUSG00000004768" "ENSMUSG00000005886" "ENSMUSG00000016918" ...
#>  $ sampleID   : Factor w/ 4 levels "group1_1","group1_2",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ counts     : num  1.1206 2.6435 3.2752 2.8726 0.0414 ...
#>  $ sampleName : Factor w/ 4 levels "group1_1","group1_2",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ description: Factor w/ 4 levels "group1_1","group1_2",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ group      : Factor w/ 2 levels "ctrl","ko": 1 1 1 1 1 1 1 1 1 1 ...
#>  $ sizeFactor : num  0.909 0.909 0.909 0.909 0.909 ...

# DESeqTransform
meltLog10(rld) %>% str()
#> 'data.frame':	841 obs. of  7 variables:
#>  $ ensgene    : chr  "ENSMUSG00000002459" "ENSMUSG00000004768" "ENSMUSG00000005886" "ENSMUSG00000016918" ...
#>  $ sampleID   : Factor w/ 4 levels "group1_1","group1_2",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ counts     : num  0.534 0.938 1.035 0.972 0.758 ...
#>  $ sampleName : Factor w/ 4 levels "group1_1","group1_2",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ description: Factor w/ 4 levels "group1_1","group1_2",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ group      : Factor w/ 2 levels "ctrl","ko": 1 1 1 1 1 1 1 1 1 1 ...
#>  $ sizeFactor : num  0.909 0.909 0.909 0.909 0.909 ...