llPostProcess: llPostProcess

In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries

Description

Post-process the output of loadMoiraiStats

Usage

llPostProcess(TABLE, TYPE = "")

Arguments

TABLE	A table output by loadMoiraiStats. Should at least contain a column called ‘samplename’.
TYPE	A type of post-processing.

Details

If the TYPE is ‘C1 96’, the sample names are assumed to be made of a run name, followed by an underscore, followed by a coordinate in 96-well plate format. These sample names are parsed to parsed to produce new columns for ‘Run’, ‘Well’, ‘Row’, ‘Column’ and ‘Chamber’ accordingly.

If the TYPE is ‘nano-fluidigm’, the generic ‘RunA’ and ‘RunB’ names are replaced with the C1 run IDs found in the RunA and RunB variables, which must exist. These new sample names are then parsed like in the ‘C1 96’ type.

See Also

loadMoiraiStats

Other smallCAGEqc metadata functions: loadMoiraiStats

Examples

libs <-
loadMoiraiStats(
    summary   = system.file("extdata/summary.txt", package="smallCAGEqc")
  , multiplex = system.file("extdata/samplename_to_sampleid.txt", package="smallCAGEqc")
  , pipeline  = "OP-WORKFLOW-CAGEscan-short-reads-v2.0" )
  
 libs %>% head
 
 # Basic processing with "C1 96" mode.
 libs %>% llPostProcess("C1 96") %>% head
 
 # More extensive processing requires RunA and RunB to be set.
 RunA <- "ID-of-Run-A"
 RunB <- NA  # No RunB in this example
 libs %>% llPostProcess("nano-fluidigm") %>% head

charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.