compareByCoord: Comparison of Samples

In FelixErnst/RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data

Comparison of Samples

Description

To compare data of different samples, a ModifierSet can be used. To select the data alongside the transcripts and their positions a GRanges or a GRangesList needs to be provided. In case of a GRanges object, the parent column must match the transcript names as defined by the out put of ranges(x), whereas in case of a GRangesList the element names must match the transcript names.

Usage

compare(x, name, pos = 1L, ...)

compareByCoord(x, coord, ...)

plotCompare(x, name, pos = 1L, normalize, ...)

plotCompareByCoord(x, coord, normalize, ...)

## S4 method for signature 'ModifierSet'
compare(x, name, pos = 1L, normalize, ...)

## S4 method for signature 'ModifierSet,GRanges'
compareByCoord(x, coord, normalize, ...)

## S4 method for signature 'ModifierSet,GRangesList'
compareByCoord(x, coord, normalize, ...)

## S4 method for signature 'ModifierSet'
plotCompare(x, name, pos = 1L, normalize, ...)

## S4 method for signature 'ModifierSet,GRanges'
plotCompareByCoord(x, coord, normalize, ...)

## S4 method for signature 'ModifierSet,GRangesList'
plotCompareByCoord(x, coord, normalize, ...)

Arguments

x	a Modifier or ModifierSet object.
name	Only for compare: the transcript name
pos	Only for compare: pos for comparison
...	optional parameters: alias a data.frame with two columns, tx_id and name, to convert transcipt ids to another identifier name Limit results to one specific gene or transcript sequenceData TRUE or FALSE? Should the aggregate of sequenceData be used for the comparison instead of the aggregate data if each Modifier element? (default: sequenceData = FALSE) compareType a valid score type to use for the comparison. If sequenceData = FALSE this defaults to mainScore(x), whereas if sequenceData = TRUE all columns will be used by setting allTypes = TRUE. allTypes TRUE or FALSE? Should all available score be compared? (default: allTypes = sequenceData) ... passed on to subsetByCoord
coord	coordinates of position to subset to. Either a GRanges or a GRangesList object. For both types the 'Parent' column is expected to match the transcript name. The GRangesList object is unlisted and only non duplicated entries are retained.
normalize	either a single logical or character value. If it is a character, it must match one of the names in the ModifierSet.

Value

compareByCoord returns a DataFrame and plotCompareByCoord returns a ggplot object, which can be modified further. The DataFrame contains columns per sample as well as the columns names, positions and mod incorporated from the coord input. If coord contains a column Activity this is included in the results as well.

Examples

data(msi,package="RNAmodR")
# constructing a GRanges obejct to mark positive positions
mod <- modifications(msi)
coord <- unique(unlist(mod))
coord$score <- NULL
coord$sd <- NULL
# return a DataFrame
compareByCoord(msi,coord)
# plot the comparison as a heatmap
plotCompareByCoord(msi,coord)

FelixErnst/RNAmodR documentation built on March 27, 2024, 2:42 a.m.