getConcordance: Get the concordance between two experiments

Description Usage Arguments Value Functions Author(s) See Also Examples

View source: R/Fluidigm-methods.R

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

1
2
3
4
5
6
7
8
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

Author(s)

Andrew McDavid

See Also

plotSCAConcordance

Examples

1
2
3
4
5
6
data(vbetaFA)
sca1 <- subset(vbetaFA, ncells==1)
sca100 <- subset(vbetaFA, ncells==100)
concord <- getConcordance(sca1, sca100)
getss(concord)
getrc(concord)

MAST documentation built on Nov. 17, 2017, 1:28 p.m.