Closed cpanse closed 3 years ago
@ mariaderrico
cat ${COMET} \
| awk -F"\t" 'NF==19{print $9"\t"$16}' \
| cut -d"," -f1 \
| sort -gr -k1 -S256M \
| awk 'BEGIN{dc=0}$2~/^REV_/{dc++}{fdr=dc/(NR-dc);print dc"\t"NR"\t"fdr}' \
| awk '$NF<0.05{print}' \
| tail
produces
251 5316 0.0495558
252 5317 0.0497532
252 5318 0.0497434
252 5319 0.0497336
253 5320 0.0499309
253 5321 0.0499211
253 5322 0.0499112
253 5323 0.0499014
253 5324 0.0498915
253 5325 0.0498817
and
library(protViz)
S <- lapply(F <- list.files(pattern="*.comet.txt"),
function(f) read.table(f, header = TRUE, fill = TRUE, skip=1))
rv <- do.call('rbind', lapply(S, protViz::summary.cometdecoy))
rv$mgf <- F
knitr::kable(rv)
results in | nPSM | psmFdrCutoff | nDecoyPSM | nConfidentPSM | nDecoyPeptide | nConfidentPeptide | nDecoyProteins | nConfidentProteins | fdrPSM | fdrPeptide | fdrProtein | mgf |
---|---|---|---|---|---|---|---|---|---|---|---|---|
52158 | 0.05 | 254 | 5327 | 199 | 3352 | 199 | 1986 | 0.0476816 | 0.0593675 | 0.1002014 | 20201022_002_S223359_474-B4.comet.txt |
5327 = 5325 + 2 Q.E.D.
https://github.com/cpanse/protViz/blob/66e5281b771fbcabd42f84d8aadbc27c275c3672/R/comet.R#L9
contradiction to the following bash code;