convertSampleInfo: Convert .raw file header information

In jasenfinch/metaboMisc: Miscellaneous Functions for Metabolomics Analyses

Convert .raw file header information

Description

Convert .raw file header information from either grover::sampleInfo(), grover::runInfo() or rawrrr::readFileHeader() into a sample information format compatible with binneR or profilePro.

Usage

convertSampleInfo(
  sample_info,
  gzip_ext = TRUE,
  user_text = c("batch", "block", "class", "rawFileOrder", "sampleOrder")
)

Arguments

sample_info	a tibble containing sample information as returned from from either grover::sampleInfo(), grover::runInfo() or rawrrr::readFileHeader()
gzip_ext	add a .gz extension to the returned mzML file names
user_text	the column names for the five ⁠User text⁠ columns

Value

A tibble containing converted sample information.

Examples

## Read the file header information from an example .raw file in the 
## grover package available from <https://jasenfinch.github.io/grover/>
sample_information <- system.file(
    'repository/Thermo-Exactive/Experiment_1/QC01.raw',
    package = 'grover') %>% 
    rawrr::readFileHeader() %>% 
    tibble::as_tibble()

## Convert the header information
converted_sample_info <- convertSampleInfo(
    sample_information,
    user_text = c('batch','block','name','class','rawFileOrder'))

converted_sample_info

jasenfinch/metaboMisc documentation built on July 31, 2023, 2:28 a.m.