qualityControl: Data Quality Control

In AurelieGuilbault/VIQCing: Data Processing For Metabolomic Data

Description

Data Quality Control

Usage

qualityControl(data, output = NULL, cohort = "", missing = 0.2,
  compound = NULL, metabolite = NULL, sampleStart = 6)

Arguments

data	name of the initial metabolomic dataset file. Must contain: a column "Compound"; a column "Metabolite"; and all the columns sample from <sampleStart> to the end of the file; the rest doesn't matter and the names "Compound" and "Metabolite" are optional, as long as the column position is specified in params. ;
output	default NULL, name of the output cleaned dataset to produce if not NULL;
cohort	default "sample", name of the sample's cohort;
compound	default NULL, position of the compound column if named otherwise;
metabolite	default NULL, position of the metabolite column if named otherwise;
sampleStart	default 6, the index of the 1st sample column.

Value

a list, containing the cleaned dataset and the QC dataframe

• dataset cleaned dataset

• QC the QC dataframe containing the columns compound, metabolite, nbna, sd, mu, CV, and remove.

Examples

for a dataset with the following header ; Compound, m/z, Metabolite, RT, Sample #1, ...
qualityControl("dummySet.txt", sampleStart = 5)

for a dataset with the following header ; compound, m/z, metabolite, RT, Sample #1, ...
qualityControl("dummySet.txt", sampleStart = 5, compound = 1, metabolite = 3)

AurelieGuilbault/VIQCing documentation built on Oct. 30, 2019, 5:02 a.m.