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

In MetaIntegrator: Meta-Analysis of Gene Expression Data

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

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"

Value

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

Author(s)

Erika Bongen

Examples

# 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

## End(Not run)

Example output

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
         Length Class  Mode
GSE13485 0      -none- NULL
GSE17156 0      -none- NULL
GSE19442 0      -none- NULL
Warning messages:
1: In .geoquery_gems_2_singlelist(originalData, formattedNames) :
  Unable to correctly download GSE13485 . Dataset will be excluded from this object.
2: In .geoquery_gems_2_singlelist(originalData, formattedNames) :
  Unable to correctly download GSE17156 . Dataset will be excluded from this object.
3: In .geoquery_gems_2_singlelist(originalData, formattedNames) :
  Unable to correctly download GSE19442 . Dataset will be excluded from this object.
Warning message:
In imputeSex(myDatasets$originalData$GSE13485) :
  Sex classification genes not present in dataset
NULL

MetaIntegrator documentation built on March 26, 2020, 6:29 p.m.