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Filter by genes belonging to a gene set from a data frame

filterGS.Rd

Filter a data frame or vector by genes belonging to a gene set

Usage

filterGS(genes, gs, mset = "all")

showModule(x, genes, gs, mset = "all", extra = NULL)

Arguments

genes

a character vector with gene IDs

gs

a character vector corresponding to the IDs of the gene sets to be shown

mset

Module set to use; see "tmodUtest" for details

x

a data frame or a vector

extra

no longer used.

Value

filterGS returns a logical vector of length equal to genes, with TRUE indicating that the given gene is a member of the gene sets in `gs`.

Details

filterGS filters a vector of gene IDs based on whether the IDs belong to a given set of gene sets, returning a logical vector.

The showModule function is deprecated and will be removed in future.

Examples

data(Egambia)
## LI.M127 – type I interferon response
sel <- filterGS("LI.M127", Egambia$GENE_SYMBOL)
head(Egambia[sel, ])
#>  [1] GENE_SYMBOL GENE_NAME   EG          NID         NID         NID        
#>  [7] NID         NID         NID         NID         NID         NID        
#> [13] NID         NID         NID         NID         NID         NID        
#> [19] TB          TB          TB          TB          TB          TB         
#> [25] TB          TB          TB          TB          TB          TB         
#> [31] TB          TB          TB         
#> <0 rows> (or 0-length row.names)