worm_cat_fun: Worm Cat Function

In dphiggs01/wormcat: Worm Gene Annotation Identifier

Worm Cat Function

Description

worm_cat_fun uses a concise list of nested categories defined in the annotation_file where each gene is first assigned to a category based on physiological function, and then to a molecular function or cellular location. worm_cat_fun output provides a scaled bubble chart that allows the visualization and direct comparison of complex datasets. The tool also provides csv files containing input gene annotations, P-values from Fisher’s exact tests, and Bonferroni multiple hypothesis testing corrections.

Usage

worm_cat_fun(
  file_to_process,
  title = "rgs",
  output_dir = NULL,
  rm_dir = FALSE,
  annotation_file = "whole_genome_v2_nov-11-2021.csv",
  input_type = "Sequence.ID",
  zip_files = TRUE
)

Arguments

file_to_process	The file name to the gene set to be processed.
title	The title for the bubble plots.
output_dir	The output directory (this is usually a relative directory from the current working directory).
rm_dir	A flag to remove the processing directory, the Default is TRUE. This assumes the zip_files is also TRUE CAUTION: If rm_dir=TRUE and zip_files=FALSE no output will be created.
annotation_file	An internal annotation file name or a path to an external annotation file.
input_type	The type of input data. 'Sequence.ID' or 'Wormbase.ID' the default is 'Sequence.ID'.
zip_files	A flag to create a zip file of the final content. The default is TRUE.

Examples

worm_cat_fun(file_to_process="WORMCAT/testdata/sams-1_up.csv", output_dir="~/wormcat_out",
             annotation_file="whole_genome_v2_nov-11-2021.csv", input_type="Wormbase.ID")

dphiggs01/wormcat documentation built on Oct. 2, 2023, 4:25 a.m.