setAlignmentRank {DIAlignR} | R Documentation |
Picks the top feature in run by comparing m-score to unaligned FDR and aligned FDR. If no satisfactory feature is found, peak-integration is carried out by mapping left and right peak boundaries from the reference feature and integrating area under the curve.
setAlignmentRank(df, refIdx, eXp, tAligned, XICs, params, adaptiveRT)
df |
(dataframe) a collection of features related to the peptide |
refIdx |
(integer) index of the reference feature in df. |
eXp |
(string) name of the run to be aligned to reference run. Must be in the rownames of fileInfo. |
tAligned |
(list) the first element corresponds to the aligned reference time, the second element is the aligned experiment time. |
XICs |
(list of dataframes) fragment-ion chromatograms of the analytes for all runs. |
params |
(list) parameters are entered as list. Output of the |
adaptiveRT |
(numeric) defines the window around the aligned retention time, within which features with m-score below aligned FDR are considered for quantification. |
XICs.eXp |
(list) list of extracted ion chromatograms from experiment run. |
invisible NULL
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2020) + GPL-3 Date: 2020-04-13
getMultipeptide, calculateIntensity, alignToRef
data(multipeptide_DIAlignR, package="DIAlignR") data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR") params <- paramsDIAlignR() df <- multipeptide_DIAlignR[["14383"]] df$alignment_rank[2] <- 1L XICs.ref <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]] XICs.eXp <- XIC_QFNNTDIVLLEDFQK_3_DIAlignR[["hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"]][["4618"]] ## Not run: # Use getAlignedTimes() to get tAligned. alignObj <- testAlignObj() tAligned <- alignedTimes2(alignObj, XICs.ref, XICs.eXp) setAlignmentRank(df, refIdx = 3L, eXp = "run2", tAligned, XICs.eXp, params, adaptiveRT = 38.66) ## End(Not run)