Commit b9685a34 authored by Sudeep Sahadevan's avatar Sudeep Sahadevan

commit before changing LICENSE

parent c1a1b2f4
Package: DEWSeq
Type: Package
Title: Differential Expressed Windows Based on Negative Binomial Distribution
Version: 1.5.6
Version: 1.6.0
Authors@R: c(
person("Sudeep", "Sahadevan", email="sahadeva@embl.de", role = c("aut","cre")),
person("Thomas", "Schwarzl", email="schwarzl@embl.de", role = c("aut", "ctb"))
......@@ -33,6 +33,8 @@ Depends:
Suggests:
knitr,
rmarkdown
VignetteBuilder:
knitr
biocViews: Sequencing,
DifferentialExpression
License: LGPL (>= 3)
......
......@@ -3,8 +3,9 @@
#' @export
#' @title windows/regions to BED
#' @description given output of \code{\link{extractRegions}}, \code{\link({resultsDEWSeq}} and significance thresholds, extract significant windows,
#' regions (merged neighboring significant windows) and create a BED file for visualization
#' @description given output of \code{\link{extractRegions}}, \code{\link({resultsDEWSeq}} and significance thresholds,
#' extract significant windows, create regions by merging adjacent significant windows.
#' Finally, write the output as a BED file for visualization
#' @param windowRes output data.frame from \code{\link{resultsDEWSeq}}
#' @param regionRes output data.frame from \code{\link{extractRegions}}
#' @param fileName filename to save BED output
......
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/toBED.R
\name{toBED}
\alias{toBED}
\title{windows/regions to BED}
\usage{
toBED(windowRes, regionRes, fileName, padjCol = "padj",
padjThresh = 0.05, log2FoldChangeCol = "log2FoldChange",
log2FoldChangeThresh = 1, trackName = "sliding windows",
description = "sliding windows")
}
\arguments{
\item{windowRes}{output data.frame from \code{\link{resultsDEWSeq}}}
\item{regionRes}{output data.frame from \code{\link{extractRegions}}}
\item{fileName}{filename to save BED output}
\item{padjCol}{name of the adjusted pvalue column (default: padj)}
\item{padjThresh}{threshold for p-adjusted value (default: 0.05)}
\item{log2FoldChangeCol}{name of the log2foldchange column (default: log2FoldChange)}
\item{log2FoldChangeThresh}{threshold for log2foldchange value (default:1)}
\item{trackName}{name of this track, for visualization}
\item{description}{description of this track, for visualization}
}
\description{
given output of \code{\link{extractRegions}}, \code{\link({resultsDEWSeq}} and significance thresholds, extract significant windows,
regions (merged neighboring significant windows) and create a BED file for visualization
}
......@@ -5,7 +5,7 @@ date: "`r format(Sys.Date(), '%m/%d/%Y')`"
abstract: >
Put abstract here
output:
BiocStyle::html_document:
rmarkdown::html_document:
highlight: pygments
toc: true
fig_width: 5
......
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