writeOutFeatureAlignmentMap: Write out alignment map to disk

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

Write out alignment map to disk

Description

Save alignment mapping to disk, either append table to OSW file, or save TSV file(s)

Usage

writeOutFeatureAlignmentMap(multiFeatureAlignmentMap, oswMerged, fileInfo)

Arguments

multiFeatureAlignmentMap	(list) contains multiple data-frames that are collection of experiment feature ids mapped to corresponding reference feature id per analyte. This is an output of getRefExpFeatureMap.
oswMerged	(logical) TRUE if merged file from pyprophet is used.
fileInfo	(data-frame) Output of DIAlignR::getRunNames function

Value

Saves the alignment feature id mapping table.

The mapping table will have the following columns:

ALIGNMENT_GROUP_ID: (int) An interger number that identifies the group of experiments that are aligned per best representative precursor (peptide).

REFERENCE: (logical int) A logical interger, 1 indicates the feature used as the reference, 0 indicates the experiment feature being aligned to reference.

FEATURE_ID: (int64) Feature id derived from OpenSwathWorkflow's peak-group picking annotation, in OSW file.

Writing to disk will be one of two possible outcomes:

1. If fileInfo contains a merged OSW, then the alignment map table will be written to the sqlite database as ALIGNMENT_GROUP_FEATURE_MAPPING.

or

2. If fileInfo does not contain a merged OSW, then the alignment map table will be written to a TSV file.

Author(s)

Justin Sing, [e-mail]

ORCID: 0000-0003-0386-0092

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

See Also

getRefExpFeatureMap, getRunNames

Examples

data(oswFiles_DIAlignR, , package="DIAlignR")
## Not run: 
writeOutFeatureAlignmentMap(multiFeatureAlignmentMap, oswMerged, fileInfo)

## End(Not run)

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