Meta_feature_list_fun: Meta_feature_list_fun

In MASHUOA/HiTMaP: A collection of tools for imaging MS data processing

Meta_feature_list_fun

Description

This is a function that prepare the candiate list for maldi imaging data qualitative or quantitative analysis. this function will read the candidate list file and generate mz for the adducts list defined in "adducts".

Usage

Meta_feature_list_fun(
  database,
  workdir = getwd(),
  adducts = c("M-H", "M+Cl"),
  cal.mz = TRUE,
  bypass = FALSE,
  BPPARAM = bpparam()
)

Arguments

database	the file name of candidate list
workdir	the folder that contains candidate list
adducts	the adducts list to be used for generating the PMF search candidates
cal.mz	If set with "TRUE", the function will recalculate the mz value according to the column named "formula" in the database and the specified adducts.
BPPARAM	parallel processing parameter for BiocParallel
mzlist_bypass	Set "TRUE" if you want to bypass the mzlist generating process, the function will keep the mz and adduct as it is for the furture analysis. Be sure that the table contains "mz", "adduct" and "moleculeNames" as they are essential for later steps.

Value

a table of candiate list

Examples

Meta_feature_list_fun(database="lipid candidates.csv",adducts=c("M-H","M+Cl"))

MASHUOA/HiTMaP documentation built on Nov. 14, 2024, 5:23 p.m.