rqcFileHeatmap: Heatmap of distance matrix of top over-represented reads

In Rqc: Quality Control Tool for High-Throughput Sequencing Data

Description

This function plots a heatmap of distance matrix of top over-represented reads. This function does not work with list of RqcResultSet objects, only with one RqcResultSet object.

Usage

rqcFileHeatmap(rqcResultSet, dist.method = "euclidean",
  hclust.method = "ward.D")

Arguments

rqcResultSet	RqcResultSet object created by rqc and rqcQA functions.
dist.method	the distance measure to be used by dist function.
hclust.method	the agglomeration method to be used by hclust function.

Value

Plot object from ggplot function.

Author(s)

Welliton Souza

Examples

checkpoint("Rqc", path=system.file(package="Rqc", "extdata"), {
  folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
  files <- list.files(full.names=TRUE, path=folder)
  rqcResultSet <- rqcQA(files, pair=c(1,1), workers=1)
}, keep="rqcResultSet")
rqcFileHeatmap(rqcResultSet[[1]])

Rqc documentation built on Nov. 8, 2020, 5:11 p.m.