Subset a qseaSet by samples

Restrict a qseaSet to a specified set of samples. All internal matrices and slots are subset consistently. Use exactly one of samplesToKeep or samplesToDrop.

subsetQset(qseaSet, samplesToKeep = NULL, samplesToDrop = NULL)

Arguments

qseaSet

qseaSet A qseaSet object containing methylation-enriched sequencing data.

samplesToKeep

character() Names of samples to retain. Cannot be used together with samplesToDrop. Default: NULL.

samplesToDrop

character() Names of samples to remove. Cannot be used together with samplesToKeep. Default: NULL.

Value

A qseaSet object:

• subsetQset(): returns the input qseaSet restricted to the selected samples.

Examples

data(exampleTumourNormal, package = "mesa")

# Keep only two samples
subsetQset(exampleTumourNormal, samplesToKeep = c("Colon1_T", "Colon1_N"))
#> qseaSet
#> =======================================
#> 2 Samples: 
#> Colon1_T, Colon1_N
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38

# Drop one sample
subsetQset(exampleTumourNormal, samplesToDrop = "Lung1_N")
#> qseaSet
#> =======================================
#> 9 Samples: 
#> Colon1_N, Colon1_T, Colon2_N, Colon2_T, Lung1_T, Lung2_N, Lung2_T, Lung3_N, Lung3_T
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38