hist_scores: Plots the distribution of scores following an GOexpress...

In kevinrue/GOexpress-original: Visualise microarray and RNAseq data using gene ontology annotations

Description

Plots the an histogram representing the frequencies of scores in the output variable of the GO_analyse() function.

This function can also be used on the output of subset_scores() function as it returns a value formatted identically to the output of the GO_analyse() function.

Usage

hist_scores(result,
            main=paste("Distribution of average scores in",
                        deparse(substitute(result))),
            xlab="Average score", ...)

Arguments

result	The output of the GO_analyse() function.
main, xlab	These arguments to title have useful defaults here.
...	Additional arguments passed on to hist().

Value

Returns the output of the hist() function.

Author(s)

Kevin Rue-Albrecht

See Also

Method hist, and GO_analyse.

Examples

# load the sample output data with p.values computed
data(AlvMac_results.pVal)

# Histogram of scores (labelled with counts)
hist_scores(result=AlvMac_results, breaks=20, labels=TRUE)

# filter for Biological Processes associated with 5+ genes and <=0.05 P-value
filtered_results <- subset_scores(
    result=AlvMac_results.pVal, total_count=5, p.val=0.05,
    namespace="BP")

# Histogram of scores (labelled with counts)
hist_scores(result=filtered_results, breaks=20, labels=TRUE)

kevinrue/GOexpress-original documentation built on May 20, 2019, 9:07 a.m.