FSWE.addSoftwareConfiguration: FSWE.addSoftwareConfiguration
In IFIproteomics/LFQbench: Label Free Quantitation benchmark package

FSWE.addSoftwareConfiguration

R Documentation

FSWE.addSoftwareConfiguration

Description

add a new software and its parameters to the list of softwares

Usage

FSWE.addSoftwareConfiguration(softwareName, input_format = "wide",
  input.extension = "*.csv$", nastrings = "NA", protein_input = F,
  filename.var = NA, quantitative.var = NA, quantitative.var.tag = NA,
  protein.var = NA, sequence.mod.var = NA, charge.var = NA,
  decoy.var = NA, decoy.tags = c("DECOY_", "reverse"), fdr.var.tag = NA,
  qvalue.var = NA, q_filter_threshold = NA, sheet.data = NA,
  sheet.fdr = NULL)

Arguments

`softwareName`	: a name for this configuration set.
`input_format`	: data format of the file. Options: "wide", "long"
`input.extension`	: file extension. Warning: FSWE interprets file extensions to read the files. Ensure that files named i.e. ".tsv" are actually tab separated values files. Do not use the extension ".xls" in tab separated values files.
`nastrings`	: string used at the file to label not available / not a number data. Examples: "NA", "#N/A", "NaN".
`protein_input`	: Boolean. Set to TRUE if the files contain only protein information (no sequence/precursors reports).
`filename.var`	: when using "long" report formats, column head name of the injection file names.
`quantitative.var`	: column head name of the quantitative values.
`quantitative.var.tag`	: when using "wide" report formats, indicate a common tag for all quantitative columns.
`protein.var`	: column head name of the protein names. It must contain a species tag.
`sequence.mod.var`	: column head name of the sequence (including modifications).
`charge.var`	: column head name of the precursor charge state.
`decoy.var`	: (optional) column head name of is_decoy (yes/no)
`decoy.tags`	: vector of tags for decoy proteins/peptides. Example: c("DECOY_", "reverse")
`fdr.var.tag`	: when using excel formats (SWATH 2.0), indicate a tag to locate the FDR columns.
`qvalue.var`	: (optional) If filtering by Q-value is required, column head name of the Q-Value.
`q_filter_threshold`	: (optional) Q-value threshold, if you want to filter results by Q-value. Note that you must specify then the qvalue.var (see above).
`sheet.data`	: when using excel formats, name of the sheet containing the quantitative values.
`sheet.fdr`	: when using excel formats, name of the sheet containing the False Discovery Rate values.