In UNIL-PAF/PAFcontaminants: Identify and remove contaminants

At the Protein Analysis Faciltiy of the University of Lausanne we have our internal list of contaminants.

Since it is a very common task to remove contaminants from MaxQuant outputs (proteinGroups.txt) we implemented a function to find the contaminants in a given file:

# load results from MQ
pg_path <- "proteinGroups.txt"
pg <- read.table(proteinGroups_path, quote='\"', row.names=NULL, header=TRUE, sep='\t', fill=TRUE, na.strings=c('Non Num\303\251rique'))

# remove contaminants
is_contaminant <-contaminants_MQ(pg)
pg_filtered <- pg[! is_contaminant,]

Alternatively you can find contaminants from a vector of either protein ACs, gene names or a given term (e.g. from a FASTA header):

# by protein AC
contaminant_AC(c("A0AVF1", "Q9NZT1", "P02786"))

# by gene name
contaminant_gene(c("TFRC", "TGM1", "MTFR1"))

# by term
contaminant_term(c("blibla", "blibla keratin blabla", "Keratinblibla", "kerami mouou"))

UNIL-PAF/PAFcontaminants documentation built on May 24, 2019, 9:50 a.m.