cyclicSigset: as in Bakken et al. (2017 PMID 29322913) create gene...

In ontoProc: processing of ontologies of anatomy, cell lines, and so on

Description

as in Bakken et al. (2017 PMID 29322913) create gene signatures for k cell types, each of which fails to express all but one gene in a set of k genes

Usage

cyclicSigset(
  idvec,
  conds = c("hasExp", "lacksExp"),
  tags = paste0("CL:X", 1:length(idvec))
)

Arguments

idvec	character vector of identifiers, must have names() set to identify cells bearing genes
conds	character(2) tokens used to indicate condition to which signature element contributes
tags	character vector of cell-type identifiers; for Cell Ontology use CL: as prefix, one element for each element of idvec

Value

a long data.frame

Examples

sigels = c("CL:X01"="GRIK3", "CL:X02"="NTNG1", "CL:X03"="BAGE2", 
        "CL:X04"="MC4R", "CL:X05"="PAX6", "CL:X06"="TSPAN12", "CL:X07"="hSHISA8", 
     "CL:X08"="SNCG", "CL:X09"="ARHGEF28", "CL:X10"="EGF")
sigdf = cyclicSigset(sigels)
head(sigdf)

ontoProc documentation built on Nov. 8, 2020, 4:49 p.m.