pattern_search: pattern_search

In OmicInt: Omics Network Exploration

Description

pattern_search function searches for gene patterns that were upregulated or downregulated throughout the conditions when comparing to the geometric mean across all conditions. The geometric mean serves as a base value to compare across multiple conditions if more complex patterns exist and also allows for a universal baseline. Function takes path variables to data frames for normalised gene counts and meta data file (CSV format) as well as an additional variable that describes the name of a column that contains the condition under the investigation.

Usage

pattern_search(data, meta, Condition = "Condition_1")

Arguments

data	Requires a path variable to a data frame of normalised scores in CSV format; class - string
meta	Requires a path variable to a data frame of metadata in CSV format; class - string
Condition	Requires a condition name to select if there are multiple conditions in meta data file, default "Condition_1"; class - string

Value

a list variable which contains a pattern list with pattern names and associated genes; class - list

Examples

## Not run: 
path_to_test_data<- system.file("extdata", "normalised_counts.csv", package="OmicInt")
path_to_meta_data<- system.file("extdata", "meta_data.csv", package="OmicInt")
# basic usage of pattern_search
pattern_search(path_to_test_data,path_to_meta_data)
## End(Not run)

OmicInt documentation built on Oct. 28, 2021, 5:09 p.m.