library("prolfquapp")
# example code
annot <- data.frame(
file = c("a1.raw", "a2.raw", "a3.raw", "a4.raw"),
name = c("aa", "ba", "aa", "ba"),
group = c("a", "a", "b", "b")
)
annot <- read_annotation(annot, QC = TRUE)
preprocess_functions <- prolfquapp::prolfqua_preprocess_functions[["DUMMY"]]
res <- preprocess_software(".", annot, preprocess_functions)
xx <- prolfquapp::ExternalReader$new()
xx$extra_args <- "list()"
xx$get_files <- "prolfquapp::get_dummy_files"
xx$preprocess <- "prolfquapp::preprocess_dummy"
res <- preprocess_software(".", annotation = annot, preprocess_functions = xx)
xx <- prolfquapp::ExternalReader$new()collects preprocess methods for various software
Description
collects preprocess methods for various software
Usage
preprocess_software(
indir,
annotation,
preprocess_functions,
pattern_contaminants = "^zz|^CON|Cont_",
pattern_decoys = "^rev_|^REV_",
nr_peptides = 1,
extreader = NULL
)
Arguments
indir
|
input directory with quantification data |
annotation
|
annotation list from read_annotation |
preprocess_functions
|
list or R6 object with get_files, preprocess, extra_args |
pattern_contaminants
|
regex pattern for contaminants |
pattern_decoys
|
regex pattern for decoys |
nr_peptides
|
minimum number of distinct (stripped) peptides per parent protein; forwarded only to readers that declare an ‘nr_peptides’ argument. Readers without it are warned about (and left unfiltered) when ‘nr_peptides > 1’. Default 1 (no filtering). |
extreader
|
optional external reader configuration |
Value
A list with xd, the reader result, and files, the discovered quantification and annotation file paths.