computeSCR: Compute the sample over carrier ratio (SCR)
In UCLouvain-CBIO/scp: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

computeSCR

R Documentation

Compute the sample over carrier ratio (SCR)

Description

The function computes the ratio of the intensities of sample channels over the intentisty of the carrier channel for each feature. The ratios are averaged within the assay.

Usage

computeSCR(
  object,
  i,
  colvar,
  samplePattern,
  sampleFUN = "mean",
  carrierPattern,
  carrierFUN = sampleFUN,
  rowDataName = "SCR"
)

Arguments

`object`	A `QFeatures` object.
`i`	A `character()` or `integer()` indicating for which assay(s) the SCR needs to be computed.
`colvar`	A `character(1)` indicating the variable to take from `colData(object)` that gives the sample annotation.
`samplePattern`	A `character(1)` pattern that matches the sample encoding in `colvar`.
`sampleFUN`	A `character(1)` or `function` that provides the summarization function to use (eg mean, sum, media, max, ...). Only used when the pattern matches multiple samples. Default is `mean`. Note for custom function, `na.rm = TRUE` is passed to `sampleFUN` to ignore missing values, make sure to provide a function that accepts this argument.
`carrierPattern`	A `character(1)` pattern that matches the carrier encoding in `colvar`. Only one match per assay is allowed, otherwise only the first match is taken
`carrierFUN`	A `character(1)` or `function` that provides the summarization function to use (eg mean, sum, media, max, ...). Only used when the pattern matches multiple carriers. Default is the same function as `sampleFUN`. Note for custom function, `na.rm = TRUE` is passed to `carrierFUN` to ignore missing values, make sure to provide a function that accepts this argument.
`rowDataName`	A `character(1)` giving the name of the new variable in the `rowData` where the computed SCR will be stored. The name cannot already exist in any of the assay `rowData`.

Value

A QFeatures object for which the rowData of the given assay(s) is augmented with the mean SCR.

Examples

data("scp1")
scp1 <- computeSCR(scp1, 
                   i = 1,
                   colvar = "SampleType",
                   carrierPattern = "Carrier",
                   samplePattern = "Blank|Macrophage|Monocyte",
                   sampleFUN = "mean",
                   rowDataName = "MeanSCR")
## Check results
rowData(scp1)[[1]][, "MeanSCR"]

UCLouvain-CBIO/scp documentation built on Oct. 12, 2024, 2:37 a.m.