FragPipe read FragPipe combined protein files up to Version 15

FragPipe read FragPipe combined protein files up to Version 15

Usage

tidy_FragPipe_combined_protein_deprec(
  combprot,
  intnames = c("total.intensity", "unique.intensity", "razor.intensity",
    "total.ion.count", "unique.ion.count", "razor.ion.count", "total.spectral.count",
    "unique.spectral.count", "razor.spectral.count"),
  protIDcol = "protein.group",
  subgroup = "subgroup",
  as_list = FALSE
)

Arguments

combprot

path to combined_protein.tsv file

intnames

intensity column prefix

protIDcol

default protein.group

subgroup

default subgroup

See also

Other FragPipe: FragPipe, tidy_FragPipe_MSstats_csv(), tidy_FragPipe_combined_protein()

Examples

prottsv <- prolfqua::find_package_file("prolfquapp", "samples/FragPipe/combined_protein_small.tsv")

prot <- tidy_FragPipe_combined_protein_deprec(prottsv)
#> annotation columns : protein.group
#> subgroup
#> protein
#> protein.id
#> entry.name
#> gene.names
#> protein.length
#> coverage
#> organism
#> protein.existence
#> description
#> protein.probability
#> top.peptide.probability
#> unique.stripped.peptides
#> summarized.total.spectral.count
#> summarized.unique.spectral.count
#> summarized.razor.spectral.count
#> Joining with `by = join_by(protein.group, subgroup, raw.file)`
#> Joining with `by = join_by(protein.group, subgroup, raw.file)`
#> Joining with `by = join_by(protein.group, subgroup, raw.file)`
#> Joining with `by = join_by(protein.group, subgroup, raw.file)`
#> Joining with `by = join_by(protein.group, subgroup, raw.file)`
#> Joining with `by = join_by(protein.group, subgroup, raw.file)`
#> Joining with `by = join_by(protein.group, subgroup, raw.file)`
#> Joining with `by = join_by(protein.group, subgroup, raw.file)`
#> Joining with `by = join_by(protein.group, subgroup)`
stopifnot( dim(prot) ==c(19980,27))