MetaIntegrator (version 2.1.3)

imputeSex: Imputes biological sex of each sample in a Dataset object

Description

Imputes biological sex of each sample in a Dataset object

Usage

imputeSex(myDataset, femGenes = NULL, malGenes = NULL)

Arguments

myDataset

datasetObject

femGenes

vector of gene symbols of genes higher expressed in females. Defaults to NULL

malGenes

vector of gene symbols of genes higher expressed in males. Defaults to NULL

Value

a vector indicating whether each sample is classified as "male" or "female"

Details

Imputes the sex of each sample in a Dataset object by performing K means clustering. If genes higher expressed in females (femGenes) and genes higher expressed in males (malGenes) are not supplied, then clustering is performed on a default set of known X-escape genes (Tukiainen et al. 2017 Nature) and Y-chromosome genes. Genes were chosen as a subset of the immune Sex Expression Signature (iSEXS) (Bongen et al. In Prep.)

Known X-Escape genes: "XIST","RPS4X","CD40LG","ZRSR2","EFHC2","CA5B","ZFX","EIF1AX","CA5BP1","UBA1","SYAP1","DDX3X","FUNDC1","USP9X","SMC1A","NUP62CL","NAA10"

Y-Chromosome genes: "KDM5D","RPS4Y1","EIF1AY","USP9Y","DDX3Y","UTY","PRKY","ZFY","TMSB4Y"

Examples

# NOT RUN {
# Add sex labels to your dataset of choice
# }
# NOT RUN {
myDatasets = getGEOData(c("GSE13485","GSE17156","GSE19442"))
myDatasets$originalData$GSE13485$pheno$sex = imputeSex(myDatasets$originalData$GSE13485)
myDatasets$originalData$GSE13485$pheno$sex
# }