read_uniprotdt: Read fasta hdrs

In bhagwataditya/importomics: Unified Statistical Modeling of Omics Data

Read fasta hdrs

Description

Read fasta hdrs

Usage

read_uniprotdt(fastafile, fastafields = FASTAFIELDS, verbose = TRUE)

parse_maxquant_hdrs(fastahdrs)

read_contaminantdt(force = FALSE, verbose = TRUE)

Arguments

fastafile	string (or charactervector)
fastafields	charactervector : which fastahdr fields to extract ?
verbose	bool
fastahdrs	character vector
force	whether to overwrite existing file

Value

data.table(uniprot, protein, gene, uniprot, reviewed, existence)

Note

existence values are always those of the canonical isoform (no isoform-level resolution for this field)

Examples

# uniprot hdrs
     fastafile <- system.file('extdata/uniprot_hsa_20140515.fasta', package = 'autonomics')
     read_uniprotdt(fastafile)
     
# maxquant hdrs
    file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
    dt <- .read_maxquant_proteingroups(file)
    parse_maxquant_hdrs(dt$`Fasta headers`)

    profile <- system.file('extdata/billing19.proteingroups.txt', package = 'autonomics')
    fosfile <- system.file('extdata/billing19.phosphosites.txt',  package = 'autonomics' )
    prodt <- .read_maxquant_proteingroups(profile)
    fosdt <- .read_maxquant_phosphosites(fosfile, profile)
    parse_maxquant_hdrs(prodt$`Fasta headers`)
    parse_maxquant_hdrs(fosdt$`Fasta headers`)
    
# contaminant hdrs
    read_contaminantdt()

bhagwataditya/importomics documentation built on Nov. 28, 2024, 8:28 a.m.