Extract the correct reference data set

Usage

getRef(
  ref = c("Reinius", "IDOL", "IDOL_extended", "Mixed", "Cord", "DLPFC", "Middleton"),
  normType = c("None", "Noob", "Funnorm", "Quantile")
)

Arguments

ref: A character representing the reference dataset, with the options of "Reinius", "IDOL", "IDOL_extended", "Mixed", "Cord", "DLPFC", and "Middleton"
normType: a character representing the normalization method, with the options of "None", "Noob", "Funnorm", "Quantile"

Value

A list of the requested reference data set (RGchannelSet Object) and the cell types of the sample (vector of character)

Examples

# Request the IDOL reference (2016) without normalization
getRef(ref = "IDOL", normType = "None")
#> see ?FlowSorted.Blood.EPIC and browseVignettes('FlowSorted.Blood.EPIC') for documentation
#> loading from cache
#> $reference
#> class: RGChannelSet 
#> dim: 1051815 49 
#> metadata(0):
#> assays(2): Green Red
#> rownames(1051815): 1600101 1600111 ... 99810990 99810992
#> rowData names(0):
#> colnames(49): 201868500150_R01C01 201868500150_R03C01 ...
#>   201870610111_R06C01 201870610111_R07C01
#> colData names(32): Sample_Plate Sample_Well ... filenames normalmix
#> Annotation
#>   array: IlluminaHumanMethylationEPIC
#>   annotation: ilm10b4.hg19
#> 
#> $cellTypes
#> [1] "CD8T"  "CD4T"  "NK"    "Bcell" "Mono"  "Gran" 
#>