setAlignmentRank: Set Alignment rank to the aligned feature

In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Set Alignment rank to the aligned feature

Description

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.

Usage

setAlignmentRank(df, refIdx, eXp, tAligned, XICs, params, adaptiveRT)

Arguments

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 paramsDIAlignR function.
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.

Value

invisible NULL

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-04-13

See Also

getMultipeptide, calculateIntensity, alignToRef

Examples

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)

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.