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

Description Usage Arguments Value Examples

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.

1	computeSCR(obj, i, colDataCol, samplePattern, carrierPattern)

`obj`	A `QFeatures` object.
`i`	A `character()` or `integer()` indicating for which assay(s) the SCR needs to be computed.
`colDataCol`	A `character(1)` indicating the variable to take from `colData(obj)` that gives the sample annotation.
`samplePattern`	A `character(1)` pattern that matches the sample encoding in `colDataCol`.
`carrierPattern`	A `character(1)` pattern that matches the carrier encoding in `colDataCol`. Only one match per assay is allowed, otherwise only the first match is taken

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

data("scp1")
scp1 <- computeSCR(scp1, 
                   i = 1,
                   colDataCol = "SampleType",
                   carrierPattern = "Carrier",
                   samplePattern = "Blank|Macrophage|Monocyte")
## Check results
rowDataToDF(scp1, 1, ".meanSCR")