| exampleData {DiPALM} | R Documentation |
Example Data: Data for use with the DiPALM vignette
Description
A list of data objects that are used to run through the DiPALM example vignette.
Usage
data("exampleData")Format
A List of 3 objects:
$rawCounts - A data frame [42383 rows X 48 columns] containing raw counts for mRNA expression data on Brassica rapa R500.
rows : Each row represents the expression of one gene across many different samples.
columns: Each column represents a different sample. Both drought-treated and properly watered samples are present, with two replicates of each time-course. Tissue was sampled at 4-hour intervals and column names are encoded as follows: S[replicate number] [D-Drought / W-Watered] [Time - sample] Example: S2D10 is part of the second replcate of the drought data and is the 10th time-point (ZT13, 13th hour after dawn on day two).
$moduleEigengenes - A dataframe [12 rows and 90 columns] representing 90 different expression vectors that describe descrete expression patterns found in the whole dataset ($timeCourseList).
Rows: each row represents a single time-point.
Columns: each column represents a distinct expression pattern seen repeatedly in the full data.
$geneAnnotations - A data frame [42383 rows and 5 columns] giving the locations within the Brassica rapa R500 genome where each gene is found. This is in SAF format which is used by the Linux Subread software package.
rows: Each row represents a single gene.
$GeneID: (character string) Unique gene accession.
$Chr: (character string) Chromosome number.
$Start: (integer) The position where the gene starts (first basepair).
$End: (integer) The position where the gene ends (last basepair).
$Strand: (character) is the gene on the positive [+] or negative [-] strand.
Details
Raw count data was summarized by mapping RNA-seq counts to the R500 Brassica rapa genome using the hisat2 aligner. Mapped reads were counted using the featureCounts function from the Linux Subread software package.
Source
Data is from: Greenham et al., eLife 2017;6:e29655