flag_remove {msPurity} | R Documentation |
On an xcmsSet object, filter flag and remove unwanted peaks. When the peaks are removed, the the xcmsSet object can be regrouped using xcms::group. The function then checks if any blank peaks are still present and the process is repeated.
The output is a list of the updated xcmsSet object, grouped peaklist and the blank removed peaks
flag_remove( xset, pol = NA, rsd_i_blank = NA, minfrac_blank = 0.5, rsd_rt_blank = NA, ithres_blank = NA, s2b = 10, ref.class = "blank", egauss_thr = NA, rsd_i_sample = NA, minfrac_sample = 0.7, rsd_rt_sample = NA, ithres_sample = NA, minfrac_xcms = 0.7, mzwid = 0.025, bw = 5, out_dir = ".", temp_save = FALSE, remove_spectra = TRUE, grp_rm_ids = NA )
xset |
object; xcmsSet object |
pol |
str; polarity (just used for naming purpose for files being saved) [positive, negative, NA] |
rsd_i_blank |
numeric; RSD threshold for the blank |
minfrac_blank |
numeric; minimum fraction of files for features needed for the blank |
rsd_rt_blank |
numeric; RSD threshold for the RT of the blank |
ithres_blank |
numeric; Intensity threshold for the blank |
s2b |
numeric; fold change (sample/blank) needed for sample peak to be allowed. e.g. if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank = 10. 1000/10 = 100 so sample has fold change higher than the threshold and the peak is not considered a blank |
ref.class |
str; A string representing the class that will be used for the blank. |
egauss_thr |
numeric; Threshold for filtering out non gaussian shaped peaks. Note this only works if the verbose option was set for XCMS; |
rsd_i_sample |
numeric; RSD threshold for the sample |
minfrac_sample |
numeric; minimum fraction of files for features needed for the sample |
rsd_rt_sample |
numeric; RSD threshold for the RT of the sample |
ithres_sample |
numeric; Intensity threshold for the sample |
minfrac_xcms |
numeric; minfrac for xcms grouping |
mzwid |
numeric; xcms grouping parameter |
bw |
numeric; xcms grouping parameter |
out_dir |
str; out directory |
temp_save |
boolean; Assign True if files for each step saved (for testing purpsoses) |
remove_spectra |
bool; TRUE if flagged spectra is to be removed |
grp_rm_ids |
vector; vector of grouped_xcms peaks to remove (coresponds to the row from xcms::group output) |
list(xset, grp_peaklist, removed_peaks)
msPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE) xset <- xcms::xcmsSet(msPths) xset@phenoData[,1] <- c('blank', 'blank', 'sample', 'sample') xset <- xcms::group(xset) fr = flag_remove(xset)