doc says mzCandidates should be a data.frame but code expects a vector
When I run:
cand <- findCandidates(fix_files, dmz = 0.03, prefilter = c(200, 1e4), noise = 50, ppm = 20)
mzRecalibrate(
file = fix_files,
mzCandidates = cand,
ppmFind = 200,
ppmQuantile = 0.2,
ppmLimit = 30,
intensityLimit = 5e2,
calibLimit = 300,
twoStage = TRUE,
preCalibrate = TRUE,
ppmFindRough = 200,
ppmQuantileRough = 0.1,
plot = TRUE,
jpg = TRUE,
save = TRUE,
verbose = TRUE,
parallel = FALSE
)
I get:
Error in (mzPreCal >= (mzRef - dmz)) & (mzPreCal <= (mzRef + dmz)) & intBool :
dims [product 32] do not match the length of object [10724]
I dug around the code and it seems mzRecalibrate really expects mzCandidates to be a vector. Inputting cand$mz seems to work.
There is not much doc, so is this the intended way to run it?