GR_to_UM | R Documentation |
Transforms Green/Red fluorescence signals into Unmethylated/Methylated channels
GR_to_UM(Red = NULL, Grn = NULL, rgSet, what = NULL, nBeads = NULL)
Red |
Mean or SD Red fluorescence intensity matrix (probes as rows, samples as columns) |
Grn |
Mean or SD Green fluorescence intensity matrix (probes as rows, samples as columns) |
rgSet |
An rgSet object imported by minfi (see minfi::read.metharray.exp for details) |
what |
Either 'Mean', 'SD' or 'NBeads' |
nBeads |
A matrix containing the number of beads (probes as rows, samples as columns) |
Illumina DNA methylation microarrays detection rely on three types of probes:
type-I Red: 2 probes/addresses per CpG, informative on the Red channel exclusively.
type-I Green: 2 probes/addresses per CpG, informative on the Green channel exclusively.
type-II: 1 probe/address per CpG, informative in both Green and Red channels.
When what is equal to "SD" or "Mean", Methylated and unmethylated intensities are computed as followed:
Methylated | Unmethylated | |
Type-II | Green (addressA) | Red (addressA) |
Type-I Red | Red (addressB) | Red (addressA) |
Type-I Green | Green (addressB) | Green (addressA) |
Also, due to the beadchip technology, each probe has been assigned to a random number of beads. If what == "NBeads", it converts the number of beads per probe and per sample to the number of beads per CpG and per sample. This requires a criteria for type-I probes for which 2 probes target the same CpG. In this case,the minimum number between the two probes targetting a type-I probe is chosen.
A list including matrices M and U (CpGs as rows, samples as columns) when what is "Mean" or "SD" and or a matrix nBeads, containing number of beads (CpGs as rows, samples as columns) when what is equal to "NBeads".
# Read IDAT files. Without the extended option, SD cannot be acquired
rgSet <- read.metharray.exp(getwd(), extended = TRUE)
# Green/Red mean to Unmethylated/Methylated mean intensities
Grn <- assay(rgSet, "Green")
Red <- assay(rgSet, "Red")
UM <- GR_to_UM(Red = Red, Grn = Grn, rgSet = rgSet, what = "Mean")
# Green/Red SD to Unmethylated/Methylated intensity SDs
GrnSD <- assay(rgSet, "GreenSD")
RedSD <-assay(rgSet, "RedSD")
UM_SD <- GR_to_UM(Red = RedSD, Grn = GrnSD, rgSet = rgSet, what = "SD")
# nBeads in probes to nBeads per CpG
nBeads <- assay(rgSet, "NBeads")
nBeads <- GR_to_UM(nBeads = nBeads, rgSet = rgSet, what = "NBeads")
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