Convert2MummichogMetaPath: Convert mSetObj to proper format for MS Peaks to Pathways...

View source: R/meta_pathway.R

Convert2MummichogMetaPathR Documentation

Convert mSetObj to proper format for MS Peaks to Pathways module

Description

Following t-test analysis or effect size calculation, this functions converts the results from the mSetObj to the proper format for mummichog analysis.

Usage

Convert2MummichogMetaPath(
  mSetObj = NA,
  rt = FALSE,
  rds.file = FALSE,
  rt.type = "seconds",
  test = "tt",
  mode = NA
)

Arguments

mSetObj

Input the name of the created mSetObj.

rt

Logical, whether or not to include retention time information.

rds.file

Logical, if true, the "annotated_peaklist.rds" must be in the current working directory to get corresponding retention time information for the features. If not, the retention time information will be taken from the feature names. Feature names must be formatted so that the mz and retention time for a single peak is separated by two underscores. For instance, m/z of 410.2148 and retention time of 42.46914 seconds must be formatted as 410.2148__42.46914.

rt.type

Character, input whether retention time is in seconds (default as RT using MetaboAnalystR is seconds) or minutes (as from MZmine).

test

Character, input what statistical values to include in the mummichog input. For p-values and t-scores only from t-test, use "tt". For log2FC from the fold-change analsis, use "fc". For effect-sizes, use "es". For, p-values, fold-changes and effect sizes, use "all".

mode

ion mode, positive or negative

Author(s)

Jasmine Chong, Jeff Xia jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)


xia-lab/MetaboAnalystR documentation built on May 25, 2024, 8:10 p.m.