diffReport: diffReport

In slzhao/MultiRankSeq: MultiRankSeq

Description

The function will generate a report based on the result of DESeq, edgeR, and baySeq analysis.

Usage

diffReport(input = system.file("extdata", "report.Rhtml", package =
  "MultiRankSeq"), output, diffResult, rawCounts, group = c(0, 0, 0, 1, 1, 1),
  paired = NULL, exportCounts = F, useVStCount = T, useAllInHeatmap = F,
  percent = 0.05)

Arguments

input	The templet file. You don't need to specify it in most cases. A file in MultiRankSeq package will be used.
output	the path and name for report file.
diffResult	The result generated by findDiff function.
rawCounts	the count data used in analysis, which should be a matrix or a data.frame.
group	the group of count data, which should be 0 or 1. The samples labeled as 1 will be compared with samples labeled as 0.
paired	the pairs of count data. Will be NULL if no pair. For example, if sample 1 and 2 are one pair, sample 3 and 4 are another pair, the paired should be c(1,1,2,2).
exportCounts	Logical. Indicate if the raw counts will be exported in result table.
useVStCount	Logical. The DESeq2 package can apply a variance stabilizing transformation (VST) to count data, which can be used in checking outliers or clustering. This parameter indicates if the transformed counts will be used in heatmap, boxplot, and correlation in reports.
useAllInHeatmap	Logical.
percent	The percent of genes with highest SD, to be used in heatmap.

Examples

data(exampleCounts)
data(exampleCountsDiff)
diffReport(output="MultiRankSeq.html",diffResult=exampleCountsDiff,rawCounts=exampleCounts)

slzhao/MultiRankSeq documentation built on April 19, 2020, 6:14 p.m.