cluster_peak_assessment: W4M Cluster Peak Pics

In HegemanLab/w4mclstrpeakpics: W4M Cluster Peak Pics

Description

Visualize feature-peaks among a cluster of samples identified through W4M XCMS preprocessing.

Usage

cluster_peak_assessment(sample_selector_column_name = "sampleType",
  sample_selector_value = "pool", sample_metadata_path,
  variable_metadata_path, data_matrix_path, output_pdf, output_tsv,
  output_rdata = "", failure_action = print)

Arguments

sample_selector_column_name	string input: column of W4M/XCMS sampleMetadata holding selector string values (default: "sampleType")
sample_selector_value	string input: value within selector column to identify samples for analysis (default: "pool")
sample_metadata_path	string input: path to W4M/XCMS sampleMetadata tab-separated values file
variable_metadata_path	string input: path to W4M/XCMS variableMetadata tab-separated values file
data_matrix_path	string input: path to W4M/XCMS dataMatrix tab-separated values file
output_pdf	string output: path to write assessment figure PDF
output_tsv	string output: path to write assessment summary tab-separated values file
output_rdata	string output: (optional) path to write RData containing all processing and plotting intermediates
failure_action	function(msg): action to take when a failure occurs (defalut: "print")

Value

environment: env containing 'df_result' that was written to output_tsv plus all intermediate and plotted variables (see source code)

Author(s)

Art Eschenlauer, [e-mail]

See Also

https://github.com/HegemanLab/w4mclstrpeakpics

http://workflow4metabolomics.org/

HegemanLab/w4mclstrpeakpics documentation built on May 23, 2019, 10:32 p.m.