Calculations of relative aberrant exon usage amounts per sample (based on FIRMA scores)

Description

The function takes in the data.frame from 'firmaAnalysis' (containing log2 FIRMA scores for all probe sets/exons (rows) in all samples (columns)), and a number indicating which percentile value of global FIRMA scores to be used as threshold for denoting aberrant exon usage (default value '1', calculating the lower and upper 1st percentiles, indicating aberrant exon skipping and inclusion, respectively). Lower and upper percentile values are calculated and stored in the global list object 'quantiles'. Also, the total number of exons per sample denoted with aberrant exon usage (having FIRMA scores outside the indicated threshold values) is calculated and stored in the global list object 'aberrantExons'. The function returns a vector with these total sample-wise amounts of aberrant exon usage (sum of aberrant skipping and inclusion amounts) relative to the average sample-wise amount in the dataset (log2-transformed).

Usage

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    aberrantExonUsage(percentile, fs)

Arguments

percentile

This number indicates the percentile value of the global FIRMA scores to be used as threshold for denoting aberrant exon usage. Default value '1' calculates the lower and upper 1st percentiles, indicating aberrant exon skipping and inclusion, respectively.

fs

Data.frame consisting of log2 FIRMA scores for all probe sets/exons (rows) in all samples (columns). This data.frame is the output from 'firmaAnalysis'.

Value

A numeric vector with log2-transformed sample-wise amounts of aberrant exon usage relative to the average sample-wise amount in the dataset. In addition, the quantiles list object is created, which contains the threshold values for the lower and upper percentiles.

Examples

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# Calculate aberrant exon usage for each sample in the data set:
    fs <- firmaAnalysis(useToyData=TRUE)
    tra <- aberrantExonUsage(1.0, fs)
#   The aberrantExonUsage function also creates the 'quantiles' object with
#   upper and lower threshold values for accepting aberrant exon usage, and
#   the list object 'aberrantExons' with the sample-wise number of exons
#   outside the threshold values.