getConcordance {MAST} | R Documentation

## 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)

[Package MAST version 1.16.0 Index]