read_compounddiscoverer: Read compound discoverer output
In bhagwataditya/autonomics: Unified Statistical Modeling of Omics Data

read_compounddiscoverer

R Documentation

Read compound discoverer output

Description

Read compound discoverer output

Usage

read_compounddiscoverer(
  dir = getwd(),
  files = list.files(path = dir, pattern = "(RP|HILIC).*\\.csv$", full.names = TRUE),
  colname_regex = "^(.*)\\d{8,8}_+(.*)_+((HILIC|RP)(NEG|POS))\\.raw.*$",
  colname_format = function(x) stringi::stri_replace_first_regex(x, colname_regex,
    "$1$2"),
  mod_extract = function(x) stringi::stri_subset_regex(x, colname_regex) %>%
    stringi::stri_replace_first_regex(colname_regex, "$3"),
  quantity = NULL,
  nonames = FALSE,
  exclude_sname_pattern = "(blank|QC|RS)",
  subgroups = NULL,
  logbase = 2,
  impute = FALSE,
  plot = FALSE,
  label = "feature_id",
  pca = plot,
  pls = plot,
  fit = if (plot) "limma" else NULL,
  formula = ~subgroup,
  block = NULL,
  coefs = NULL,
  contrasts = NULL,
  palette = NULL,
  verbose = TRUE
)

Arguments

`dir`	compound discoverer output directory
`files`	compound discoverer output files
`colname_regex`	regular expression to parse sample names from column names
`colname_format`	function to reformat column names
`mod_extract`	function to extract MS modi from sample names
`quantity`	'area', 'normalizedarea' or NULL
`nonames`	TRUE or FALSE: retain compunds without Names?
`exclude_sname_pattern`	regular expression of sample names to exclude
`subgroups`	NULL or string vector : subgroups to retain
`logbase`	base for logarithmization of the data
`impute`	TRUE or FALSE: impute group-specific NA values?
`plot`	TRUE or FALSE: plot ?
`label`	fvar
`pca`	TRUE or FALSE: run pca ?
`pls`	TRUE or FALSE: run pls ?
`fit`	model engine: 'limma', 'lm', 'lme(r)', 'wilcoxon' or NULL
`formula`	model formula
`block`	model blockvar: string or NULL
`coefs`	model coefficients of interest: character vector or NULL
`contrasts`	coefficient contrasts of interest: character vector or NULL
`palette`	color palette : named character vector
`verbose`	TRUE or FALSE : message ?