featlistCompare: featlistCompare

In mjhelf/Mosaic: Metaboseek platform

featlistCompare

Description

compare feature tables and find molecular features that are shifted from the mz values in reflist by mzdiff and are within rtdiff.

Usage

featlistCompare(
  reflist = reflist,
  complist = complist,
  mzdiff = 2 * 1.00335,
  pktol = 2,
  rtdiff = 10,
  ppm = 5
)

Arguments

reflist	data.frame with molecular features and columns mz, rt, rtmin, rtmax
complist	data.frame with molecular features and columns mz, rt, rtmin, rtmax
mzdiff	expected mz difference between features of interest in reflist and complist
pktol	maximum fold difference in retention time peak width between matched peaks
rtdiff	maximum retention time difference (same unit as rt columns in reflist and complist, typically seconds)
ppm	maximum relative mz difference between matched peaks in parts per million (ppm)

Details

Will first find matches in complist and then go back and find the shifted mz in reflist as well as the unshifted mass in complist.

Value

a list of data.frames

Examples

## Not run: 
 MseekExamplePreload(data = TRUE, tables = TRUE)
demo_reflist = data.frame(mz = 101:200,
                     rt = 201:300,
                     rtmin = 198:297,
                     rtmax = 201:300)

demo_complist = demo_reflist

demo_complist$mz <- demo_complist$mz + rnorm(100, 2*1.00335, sd = 2*1.00335/600)

demo_complist[101:150,] <- demo_complist[1:50,]

demo_complist$mz[101:150] <- demo_complist$mz[101:150] + 1e-10


compareResults <- featlistCompare(reflist = demo_reflist, complist = demo_complist)

  MseekExamplePreload(data = FALSE, tables = TRUE)
compareResultsBig <- featlistCompare(reflist = tab2$df, complist = tab2$df)


## End(Not run)

mjhelf/Mosaic documentation built on April 28, 2022, 11:32 a.m.