In TomSmithCGAT/OptProc:

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(OptProc)
library(MSnbase)
library(camprotR)
library(tidyverse)

Define infiles

infile <- system.file("extdata","hyperLOPIT_mES_Rep1_PSMs_txt.gz", package="OptProc")
fasta_infile <- system.file("extdata", "cRAP_FullIdentifiers.fasta.gz", package="OptProc")

Make the cRAP list for filtering

bs.fasta <- Biostrings::fasta.index(fasta_infile, seqtype = "AA")

# Extract the UniProt accessions 
crap.accessions <- bs.fasta %>% 
  pull(desc) %>% 
  stringr::str_extract_all("(?<=\\|).*?(?=\\|)") %>% 
  unlist()

Parse the infile and remove features without quantification values

psm <- parse_features(read.delim(infile),
                      level='PSM',
                      TMT=TRUE,
                      crap_proteins=crap.accessions,
                      unique_master=FALSE) # requires Number.of.Protein.Groups column which isn't present

Make MSnSet

abundance_cols <- colnames(psm)[grepl('Abundance.', colnames(psm))]

psm_e <- as.matrix(psm[,abundance_cols])
psm_f <- psm[,setdiff(colnames(psm), abundance_cols)]

# update the column names to remove the 'Abundance.` prefix
colnames(psm_e) <- gsub('Abundance.', '', colnames(psm_e))

res <- MSnbase::MSnSet(exprs=psm_e, fData=psm_f)

plotNA(res)

Add missing values to 100 PSMs

add_missing_psm <- res %>% filterNA(pNA=0.4) %>% # remove features with >40% missing
  addMissing(
  n=100, # how many features to add missing values to
  id_column="Annotated.Sequence", # The fvarlabel for grouping features
  verbose=TRUE)

Impute missing values

imputed_psm_snknn <- imputeOptProc(add_missing_psm$missing, method='sn-knn', k=10, verbose=TRUE)
imputed_psm_knn <- imputeOptProc(add_missing_psm$missing, method='knn', k=10, verbose=TRUE)

Plot truth vs imputed

p <- getTruthImputed(imputed_psm_knn, add_missing_psm$missing, add_missing_psm$truth) %>%
  plotTruthImputed() + annotate(geom='text', x=-2, y=6, label='knn, k=10', size=5)

p2 <- getTruthImputed(imputed_psm_snknn, add_missing_psm$missing, add_missing_psm$truth) %>%
  plotTruthImputed() + annotate(geom='text', x=-2, y=6, label='sn-knn, k=10', size=5)

print(p)
print(p2)

TomSmithCGAT/OptProc documentation built on July 22, 2023, 12:08 a.m.