Normalise barcode counts
normaliseCounts.RdNormalise barcode counts within a DGEList object
Arguments
- dgeObject
DGEList object with barcode counts.
- method
method of normalization. One of `CPM`, `TMM`, `TMMwsp`, `upperquartile` or `RLE` (string). See `edgeR::calcNormFactors()`.
- threshold
Threshold to apply to counts before normalisation (integer). Default = `0`.
Examples
data(test.dge)
normaliseCounts(test.dge, method = "CPM", threshold = 0)
#> An object of class "DGEList"
#> $samples
#> Sample Experiment Group PCR_Replicate Treatment group
#> T0-1 T0-1 test_01 T0 1 T0 T0
#> T0-2 T0-2 test_01 T0 2 T0 T0
#> S10-1 S10-1 test_01 10_High_dose 1 High_dose 10_High_dose
#> S10-2 S10-2 test_01 10_High_dose 2 High_dose 10_High_dose
#> S11-1 S11-1 test_01 11_Vehicle 1 Vehicle 11_Vehicle
#> lib.size norm.factors
#> T0-1 3584606 1
#> T0-2 3349340 1
#> S10-1 4114186 1
#> S10-2 4196458 1
#> S11-1 2907500 1
#> 33 more rows ...
#>
#> $counts
#> Samples
#> Tags T0-1 T0-2 S10-1 S10-2 S11-1 S11-2 S12-1 S12-2 S13-1 S13-2
#> BC_1 48.81987 23.58674 0 0 0 0 0 0 0 0
#> BC_13 406.73926 249.00428 0 0 0 0 0 0 0 0
#> BC_99 322.21114 463.97201 0 0 0 0 0 0 0 0
#> BC_120 79.50665 54.93620 0 0 0 0 0 0 0 0
#> BC_351 0.00000 0.00000 0 0 0 0 0 0 0 0
#> Samples
#> Tags S14-1 S14-2 S15-1 S15-2 S16-1 S16-2 S17-1 S17-2 S18-1 S18-2 S1-1
#> BC_1 0 0 0 0 0 0 0 0 0 0 0.00000
#> BC_13 0 0 0 0 0 0 0 0 0 0 0.00000
#> BC_99 0 0 0 0 0 0 0 0 0 0 30.45571
#> BC_120 0 0 0 0 0 0 0 0 0 0 0.00000
#> BC_351 0 0 0 0 0 0 0 0 0 0 0.00000
#> Samples
#> Tags S1-2 S2-1 S2-2 S3-1 S3-2 S4-1 S4-2 S5-1 S5-2 S6-1 S6-2 S7-1 S7-2
#> BC_1 0.00000 0 0 0 0 0 0 0 0 0 0 0 0
#> BC_13 0.00000 0 0 0 0 0 0 0 0 0 0 0 0
#> BC_99 50.22587 0 0 0 0 0 0 0 0 0 0 0 0
#> BC_120 0.00000 0 0 0 0 0 0 0 0 0 0 0 0
#> BC_351 0.00000 0 0 0 0 0 0 0 0 0 0 0 0
#> Samples
#> Tags S8-1 S8-2 S9-1 S9-2
#> BC_1 0 0 0 0
#> BC_13 0 0 0 0
#> BC_99 0 0 0 0
#> BC_120 0 0 0 0
#> BC_351 0 0 0 0
#> 1634 more rows ...
#>