DRIMSeq (version 1.0.2)

dmDSdata: Create dmDSdata object Constructor function for a dmDSdata object.

Description

Create dmDSdata object Constructor function for a dmDSdata object.

Usage

dmDSdata(counts, gene_id, feature_id, sample_id, group)

Arguments

counts

Numeric matrix or data frame of counts. Rows represent features, for example, exons, exonic bins or transcripts. Columns represent samples.

gene_id

Vector of gene IDs corresponding to counts.

feature_id

Vector of feature IDs corresponding to counts.

sample_id

Vector of unique sample IDs corresponding to the columns in counts.

group

Vector that defines the grouping of samples.

Value

Returns a dmDSdata object.

See Also

plotData, dmFilter, dmDispersion, dmFit, dmTest

Examples

#############################
### Create dmDSdata object 
#############################
### Get kallisto transcript counts from 'PasillaTranscriptExpr' package

library(PasillaTranscriptExpr)

data_dir  <- system.file("extdata", package = "PasillaTranscriptExpr")

metadata <- read.table(file.path(data_dir, "metadata.txt"), header = TRUE, 
 as.is = TRUE)
metadata

counts <- read.table(file.path(data_dir, "counts.txt"), header = TRUE, 
 as.is = TRUE)
head(counts)

# Create a dmDSdata object
d <- dmDSdata(counts = counts[, metadata$SampleName], 
 gene_id = counts$gene_id, feature_id = counts$feature_id, 
 sample_id = metadata$SampleName, group = metadata$condition)

plotData(d)

# Use a subset of genes, which is defined in the following file
gene_id_subset <- readLines(file.path(data_dir, "gene_id_subset.txt"))
d <- d[names(d) %in% gene_id_subset, ]

plotData(d)