find_contrast_samples: Determine samples in selected contrast

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Determine samples in selected contrast

Description

Find the samples that are in the group of the selected contrast. Can be used to subset the data to only include the samples that correspond to the chosen comparison.

Usage

find_contrast_samples(
  select_contrast,
  all_sample_names,
  sample_info = NULL,
  select_factors_model = NULL,
  select_model_comprions = NULL,
  reference_levels = NULL,
  counts_deg_method = NULL,
  data_file_format = NULL
)

Arguments

select_contrast	String designating the comparison from DEG analysis to filter for the significant genes. See the 'comparison' element from the list returned from limma_value() for options.
all_sample_names	List of the column names of the processed gene data
sample_info	Matrix of experiment design information for grouping samples
select_factors_model	List designating the selected factors for the model expression. Example, c("P53", "Treatment"). See list_factors_ui() for specific options.
select_model_comprions	String designating selected comparisons to analyze in the DEG analysis
reference_levels	Vector of reference levels to use for the selected factors. Should be in the form of "p53: NULL vs. WT". See list_model_comparisons_ui() for specific options.
counts_deg_method	Integer indicating method of DEG analysis being performed. This should be one of 1 for limma-trend, 2 for limma-voom, and 3 for DESeq2.
data_file_format	Integer indicating the data format. This should be one of 1 for read counts data, 2 for normalized expression, or 3 for fold changes and adjusted P-values

Value

A numeric vector that can be used to index the processed data and subset to only include the columns from the selected contrast.

espors/idepGolem documentation built on April 23, 2024, 1:11 p.m.