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Find equivalent no4sU samples for 4sU samples

Source: R/dropout.R
Findno4sUPairs.Rd

Identify all no4sU samples in the same condition, and return everything as a list to be used in Plot4sUDropout, Plot4sUDropoutRank, Plot4sUDropoutAll, Plot4sUDropoutRankAll

Usage

Findno4sUPairs(data, paired.replicates = FALSE, discard.no4sU = TRUE)

Arguments

data

a grandR object

paired.replicates

pair replicates, i.e. only no4sU.A is found for 4sU.A

discard.no4sU

do not report references for no4sU samples

Value

a named list containing, for each 4sU sample, a vector of equivalent no4sU samples

See also

Plot4sUDropout, Plot4sUDropoutRank, Plot4sUDropoutAll, Plot4sUDropoutRankAll

Examples

sars <- ReadGRAND(system.file("extdata", "sars.tsv.gz", package = "grandR"),
                  design=c("Condition",Design$dur.4sU,Design$Replicate))
#> Warning: Duplicate gene symbols (n=1, e.g. MATR3) present, making unique!
Findno4sUPairs(sars)
#> $Mock.1h.A
#> [1] "Mock.no4sU.A"
#> 
#> $Mock.2h.A
#> [1] "Mock.no4sU.A"
#> 
#> $Mock.2h.B
#> [1] "Mock.no4sU.A"
#> 
#> $Mock.3h.A
#> [1] "Mock.no4sU.A"
#> 
#> $Mock.4h.A
#> [1] "Mock.no4sU.A"
#> 
#> $SARS.1h.A
#> [1] "SARS.no4sU.A"
#> 
#> $SARS.2h.A
#> [1] "SARS.no4sU.A"
#> 
#> $SARS.2h.B
#> [1] "SARS.no4sU.A"
#> 
#> $SARS.3h.A
#> [1] "SARS.no4sU.A"
#> 
#> $SARS.4h.A
#> [1] "SARS.no4sU.A"
#>