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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/post_analysis.R

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

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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

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# 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)

Example output

Loading required package: grid
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage:base:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

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GOexpress documentation built on Nov. 8, 2020, 7:45 p.m.