Get the concordance between two experiments

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.

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

See also

plotSCAConcordance

Examples

data(vbetaFA)
sca1 <- subset(vbetaFA, ncells==1)
sca100 <- subset(vbetaFA, ncells==100)
concord <- getConcordance(sca1, sca100)
#> Using primerid as id variables
#> Using primerid as id variables
getss(concord)
#> [1] 3.621746
getrc(concord)
#> [1] 0.8374755