plotTSSprecision: Compare the precision of TSS detection between multiple...

In vivekbhr/icetea: Integrating Cap Enrichment with Transcript Expression Analysis

Description

Plot precision of TSS detection from multiple samples (bed files) with respect to a given reference annotation.

Plot precision of TSS detection from multiple samples present within a CapSet object, with respect to a given reference annotation.

Usage

plotTSSprecision(
  reference,
  detectedTSS,
  distanceCutoff = 500,
  outFile = NULL,
  ...
)

## S4 method for signature 'GRanges,character'
plotTSSprecision(
  reference,
  detectedTSS,
  distanceCutoff = 500,
  outFile = NULL,
  sampleNames
)

## S4 method for signature 'GRanges,CapSet'
plotTSSprecision(
  reference,
  detectedTSS,
  distanceCutoff = 500,
  outFile = NULL,
  ...
)

Arguments

reference	Reference Transcrips/Genes as a GRanges object
detectedTSS	Either a CapSet object with TSS information (after running detectTSS) or a character vector with paths to the BED files containing detcted TSSs
distanceCutoff	integer. Maximum distance (in base pairs) from reference TSS to plot
outFile	character. Output file name (filename extention would be used to determine type) If outfile not specified, the plot would be returned on the screen
...	Additional arguments
sampleNames	character. Labels for input samples (in the same order as the input bed files)

Value

A ggplot object, or a file. Plot showing perent of TSS detected per sample with respect to their cumulative distance to TSS of the provided reference

Examples

# load a txdb object
suppressMessages(library("TxDb.Dmelanogaster.UCSC.dm6.ensGene"))
seqlevelsStyle(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "ENSEMBL"
transcripts <- transcripts(TxDb.Dmelanogaster.UCSC.dm6.ensGene)

# Plotting the precision using a pre computed set of TSS (.bed files) :

tssfile <- system.file("extdata", "testTSS_merged.bed", package = "icetea")
plotTSSprecision(reference = transcripts, detectedTSS = tssfile,
                sampleNames = "testTSS", distanceCutoff = 500,
                outFile = "TSS_detection_precision.png")

## Plotting the precision using a CapSet object :

library("TxDb.Dmelanogaster.UCSC.dm6.ensGene")
seqlevelsStyle(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "ENSEMBL"
# only use chrX to make the analysis faster
seqlevels(TxDb.Dmelanogaster.UCSC.dm6.ensGene) <- "X"
transcripts <- transcripts(TxDb.Dmelanogaster.UCSC.dm6.ensGene)

# load a previously saved CapSet object
cs <- exampleCSobject()
# plot
plotTSSprecision(reference = transcripts, detectedTSS = cs,
                  outFile = "TSS_detection_precision.png")

vivekbhr/icetea documentation built on June 8, 2020, 4:45 a.m.