Remove columns/cells/samples with NAs exceeding a threshold. See cleanAssay()

Remove columns/cells/samples with NAs exceeding a threshold. See cleanAssay()

Usage

cleanAssayCols(se, na.max = 0.8, assay = c("array", "bisulfite"))

Arguments

se: Input SummarizedExperiment object
na.max: The maximum number of NAs allowed as a fraction
assay: The type of assay we are working with

Value

A filtered matrix

Examples

if (requireNamespace("minfi", quietly = TRUE)) {
  data("array_data_chr14", package = "compartmap")
  compartmap:::cleanAssayCols(array.data.chr14, assay = "array")
}
#> Setting options('download.file.method.GEOquery'='auto')
#> Setting options('GEOquery.inmemory.gpl'=FALSE)
#> class: GenomicRatioSet 
#> dim: 15078 11 
#> metadata(1): SNPs
#> assays(2): Beta CN
#> rownames(15078): cg07948143 cg20517615 ... cg23902114 cg24746738
#> rowData names(0):
#> colnames(11): naive.1 rTreg.2 ... act_rTreg.10 birth.11
#> colData names(10): Sample_Name Sample_Well ... Basename filenames
#> Annotation
#>   array: IlluminaHumanMethylation450k
#>   annotation: ilmn12.hg19
#> Preprocessing
#>   Method: SeSAMe (type I)
#>   minfi version: 1.27.8
#>   Manifest version: 0.6.0