populateReferenceExperimentFeatureAlignmentMap: Populate Alignment Feature Mapping Table

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

Populate Alignment Feature Mapping Table

Description

Populate an alignment feature mapping table for star align method, to map aligned features in experiment runs to the reference run for a given analyte. Is a data.table generated from of getRefExpFeatureMap.

Usage

populateReferenceExperimentFeatureAlignmentMap(
  df,
  feature_alignment_mapping,
  tAligned,
  ref,
  eXp,
  analyte_chr
)

Arguments

df	(dataframe) a collection of features related to the peptide
feature_alignment_mapping	(data.table) contains experiment feature ids mapped to corresponding reference feature id per analyte. This is an output of getRefExpFeatureMap.
tAligned	(list) the first element corresponds to the aligned reference time, the second element is the aligned experiment time.
ref	(string) name of the reference run. Must be in the rownames of fileInfo.
eXp	(string) name of the run to be aligned to reference run. Must be in the rownames of fileInfo.
analyte_chr	(string) name of highest quality precursor/transition_group_id

Value

invisible NULL

Author(s)

Justin Sing, [e-mail]

ORCID: 0000-0003-0386-0092

License: (c) Author (2020) + GPL-3 Date: 2022-11-07

See Also

getRefExpFeatureMap, 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)
# Use getRefExpFeatureMap() to get a list of feature_alignment_mapping tables
feature_alignment_mapping <- data.table::as.data.table(structure(list(
reference_feature_id = structure(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), class = "integer64"),
experiment_feature_id = structure(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), class = "integer64")),
row.names = c(NA, -15L), class = c("data.table", "data.frame"), sorted = "reference_feature_id"))
populateReferenceExperimentFeatureAlignmentMap(df, feature_alignment_mapping, tAligned, ref = "run0", eXp = "run2", analyte_chr="4618")

## End(Not run)

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