chord_dat: Creates a binary matrix.

Description Usage Arguments Details Value See Also Examples

View source: R/GOCore.R

Description

The function creates a matrix which represents the binary relation (1= is related to, 0= is not related to) between selected genes (row) and processes (column). The resulting matrix can be visualized with the GOChord function.

Usage

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chord_dat(data, genes, process)

Arguments

data

A data frame with at least two coloumns: GO ID|term and genes. Each row contains exactly one GO ID|term and one gene. A column containing logFC values is optional and might be used if genes is missing.

genes

A character vector of selected genes OR data frame with coloumns for gene ID and logFC.

process

A character vector of selected processes

Details

If more than one logFC value for each gene is at disposal, only one should be used to create the binary matrix. The other values have to be added manually later.

Value

A binary matrix

See Also

GOChord

Examples

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## Not run: 
# Load the included dataset
data(EC)

# Building the circ object
circ <- circle_dat(EC$david, EC$genelist)

# Building the binary matrix
chord <- chord_dat(circ, EC$genes, EC$process)


## End(Not run)

Example output

Loading required package: ggplot2
Loading required package: ggdendro
Loading required package: gridExtra
Loading required package: RColorBrewer

GOplot documentation built on May 29, 2017, 11:17 p.m.