getConcordance: Get the concordance between two experiments

In RGLab/MAST: Model-based Analysis of Single Cell Transcriptomics

Get the concordance between two experiments

Description

Return the concordance between two assays (i.e. single cell and hundred cell). The "average" of singleCellRef (after adjusting for the number of cells) and singleCellComp are taken per gene, per groups. A data.frame with one row per gene-groups is returned with some additional columns.

Usage

getConcordance(
  singleCellRef,
  singleCellcomp,
  groups = NULL,
  fun.natural = expavg,
  fun.cycle = logmean
)

getwss(concord, nexp)

getss(concord)

getrc(concord)

Arguments

singleCellRef	"reference" SingleCellAssay
singleCellcomp	"comparison" SingleCellAssay
groups	character vector giving variable(s) on which the comparison is conditioned
fun.natural	function to transform the SingleCellAssays to a mRNA proportional level
fun.cycle	inverse function of fun.natural
concord	data.frame returned by getConcordance
nexp	number of expressed cells per row in concord

Value

concordance between two assays

Functions

• getwss(): getrc the sum of squares, weighted by nexp

• getss(): return the sum of squares

• getrc(): Return Lin's (1989) concordance correlation coefficient

Author(s)

Andrew McDavid

See Also

plotSCAConcordance

Examples

data(vbetaFA)
sca1 <- subset(vbetaFA, ncells==1)
sca100 <- subset(vbetaFA, ncells==100)
concord <- getConcordance(sca1, sca100)
getss(concord)
getrc(concord)

RGLab/MAST documentation built on Sept. 30, 2023, 1:08 p.m.