OmicsoftToDgeObj: Function OmicsoftToDgeObj

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Build a DGEobj from Omicsoft output or tabbed text files.

Usage

OmicsoftToDgeObj(
  counts = "RNA-Seq.Count.Table.txt",
  seqAnnotation = "RNA-Seq.Count.Annotation.txt",
  design = "RNA-Seq.Design.txt",
  level = "gene",
  source = "Omicsoft",
  path = ".",
  customAttr,
  gz = FALSE
)

Arguments

counts	A text file name for count data (gene rows by sample columns) (required) [Default = "RNA-Seq.Count.Table.txt"]
seqAnnotation	Filename for Gene, isoform or exon level (row) annotation (required) [Default = "RNA-Seq.Count.Annotation.txt"]
design	Filename for sample annotation with expt factors and other sample-associated data (required) [Default = RNA-Seq.Design.txt"]
level	One of "gene", "isoform", "exon" (required) [Default = "gene"]
source	Default = "Omicsoft. Change if your data if from somewhere else.
path	File path for the three data files (Default = "./")
customAttr	A named list of custom attributes to attach to the DGEobj; Optional but highly encouraged; suggestions: list(PID = "20170101-0001", XpressID = "123456", Genome = "Mouse.B38", GeneMobel = "Ensembl.R84")

Details

User provides separate tab-delimited text files for row (gene) annotation, column (sample) anotation and "assays" (matrices of RxC e.g. counts, FPKM, etc).

Two global variables hold the names of the Omicsoft data files; .geneData and .isoformData.

Data Requirements:

Assay data should have rownames (sequence ids) and column names (sample IDs). Sequence annotation should also have the same rownames as assays.

If possible, the sequence annotation should include chromosome position data (chr, start, end, strand).

Sample annotation is one row for each column in the count table. rownames(sampleannotation) == colnames(counts).

Function DGEobj::annotateDGEobj provides an easier way than the customAttr argument here. annotateDGEobj reads key=value pairs from a text file to define attributes.

Value

A DGEobj

Author(s)

John Thompson, [e-mail]

Examples

#Defaults set for an omicsoft dataset:
MyDgeObj <- OmicsoftToDgeObj (customAttr=list(
                                   PID = "20170101-0001",
                                   XpressID = "123456",
                                   Genome = "Mouse.B38",
                                   GeneMobel = "Ensembl.R84")

#I have data files from somewhere else
MyDgeObj = OmicsoftToDgeObj (MyCounts, MyGeneAnnotation, MyDesign,
                                   level = "gene",
                                   customAttr = list(
                                      PID = "20170101-0001",
                                      XpressID = "123456",
                                      Genome = "Mouse.B38",
                                      GeneMobel = "Ensembl.R84")
                             )

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.