mergeXIC: Merge two XICs into one

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

Merge two XICs into one

Description

Both extracted-ion chromatograms must have same number of rows. Missing values are not allowed. Intensities are weighted-averaged.

Usage

mergeXIC(XIC.ref, XIC.eXp, wRef, mergeStrategy)

Arguments

XIC.ref	(data-frame) extracted ion chromatogram from reference run. Must not contain missing values.
XIC.eXp	(data-frame) extracted ion chromatogram from experiment run. Must not contain missing values.
wRef	(numeric) Weight of the reference XIC. Must be between 0 and 1.
mergeStrategy	(string) must be either ref, avg, refStart or refEnd.

Value

(dataframe) has two columns:

time	(numeric)
intensity	(numeric)

time-merging

There are three startegies for calculating time to keep sampling rate equal to parents:
- Use reference time.
- Average time (Non-gap region will have parent's sampling rate).
- Start/end with the average then fixed sampling rate.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-05-23

See Also

childXIC, alignedXIC

Examples

data(XIC_QFNNTDIVLLEDFQK_3_DIAlignR, package="DIAlignR")
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"]][["14299_QFNNTDIVLLEDFQK/3"]]
## Not run: 
plot(mergeXIC(XICs.ref[[1]], XICs.eXp[[1]], wRef = 0.5, mergeStrategy = "ref"), type = "l")

## End(Not run)

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.