corTools (version 1.0)

cytosub: Dataset Subsetter

Description

Subsets a dataset based on text common to the traits that should be removed. Built with Cytoscape datasets in mind, to reduce the complexity of Cytoscape networks.

Usage

cytosub(dat, col1, col2, text)

Arguments

dat

Dataset containing the traits

col1

Column 1 of the dataset, containing trait names, such as a source interaction in Cytoscape.

col2

Column 2 of the dataset, containing trait names, such as a target interaction in Cytoscape.

text

Text common to the traits that need to be edited out of the dataset. Regular expressions can also be entered.

Value

Details

This function is built to help interpret GWAS result data by considering relationships between associated genes or traits. It requires the basic input of a network of binary relationships between traits, with two columns of trait names and a third column of the trait interaction. This interaction could be multiple things, such as trait-trait relationships in a pathway, or trait correlation data. This data can be inputted directly into Cytoscape for the visualization of these interaction networks, however for a large network it is useful to pare down the number of interactions. This function subsets the user-inputted data. Function will preserve columns (such as trait values), but delete rows corresponding to unwanted traits. Regular expressions can also be entered in addition to regular text. Function uses grepl to text-match to find traits that the user would like to subset out, so regular expressions can also be entered.

References

http://www.cytoscape.org/ Krouk G, Mirowski P, LeCun Y, Shasha DE, Coruzzi GM (2010) Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol 11(12):R123.

Examples

# Create sample dataset
source.interaction <- c("R1", "R2", "R3", "E1", "E2")
target.interaction <- c("L1", "L2", "L4", "E6", "E7")
values.interaction <- c(1.42, 14.34, 6.43, 32.1, 15.8)
dataset <- cbind(source.interaction, target.interaction, values.interaction)

cytosub(dataset, source.interaction, target.interaction, E)
# dataset indicates the data we are working with
# source.interaction and target.interaction denote the columns of the dataset
# E indicates the text that we want to search for and edit out of the dataset
# function will return the dataset without "E1", "E2", "E6", "E7"