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

rqcFileHeatmap {Rqc}

R Documentation

Heatmap of distance matrix of top over-represented reads

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]])

[Package Rqc version 1.16.2 Index]