annotate_maxquant: Annotate maxquant

In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

Annotate maxquant

Description

Annotate maxquant data.table

Usage

annotate_maxquant(
  dt,
  uniprothdrs,
  contaminanthdrs,
  maxquanthdrs,
  restapi = FALSE,
  verbose = TRUE
)

Arguments

dt	data.table : output of read_maxquant_(proteingroups|phosphosites)
uniprothdrs	data.table : output of read_uniprotdt
contaminanthdrs	data.table : output of read_uniprotdt
maxquanthdrs	data.table : output of read_uniprotdt
restapi	logical(1) : use uniprot restapi to complete missing annotations ?
verbose	logical(1) : message ?

Details

Uncollapse, annotate, curate, recollapse, name

Value

data.table

Examples

# Fukuda 2020: contaminants + maxquanthdrs
#-----------------------------------------
          file <- system.file('extdata/fukuda20.proteingroups.txt', package = 'autonomics')
            dt <- .read_maxquant_proteingroups(file)
            dt[, 1:2]
     uniprothdrs <- NULL
 contaminanthdrs <- read_contaminantdt()
    maxquanthdrs <- parse_maxquant_hdrs(dt$`Fasta headers`); dt$`Fasta headers` <- NULL
          dt %<>% annotate_maxquant(uniprothdrs, contaminanthdrs, maxquanthdrs)
          dt[                 , 1:9]
          dt[    reverse== '+', 1:9]
          dt[contaminant== '+', 1:9]
                                              
# Billing 2019: uniprothdrs + contaminants + maxquanthdrs
#--------------------------------------------------------
profile <- system.file('extdata/billing19.proteingroups.txt', package = 'autonomics')
fosfile <- system.file('extdata/billing19.phosphosites.txt',  package = 'autonomics')
 upfile <- system.file('extdata/uniprot_hsa_20140515.fasta',  package = 'autonomics')
prodt <- .read_maxquant_proteingroups(profile);         prodt[, 1:2]
fosdt <- .read_maxquant_phosphosites(fosfile, profile); fosdt[, 1:3]
    uniprothdrs <- read_uniprotdt(upfile)
contaminanthdrs <- read_contaminantdt()
   maxquanthdrs <- parse_maxquant_hdrs(prodt$`Fasta headers`)
annotate_maxquant(prodt, uniprothdrs, contaminanthdrs, maxquanthdrs)[, 1:8]
annotate_maxquant(fosdt, uniprothdrs, contaminanthdrs, maxquanthdrs)[, 1:8]

bhagwataditya/autonomics documentation built on Dec. 1, 2024, 12:27 a.m.