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

Description Usage Arguments Value Examples

View source: R/CLextend.R

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

1
2
3
4
5
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

1
2
3
4
5
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.