dmDSdata: Create dmDSdata object

In gosianow/DRIMSeq: Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Description

Constructor function for a dmDSdata object.

Usage

dmDSdata(counts, samples)

Arguments

counts	Data frame with counts. Rows correspond to features, for example, transcripts or exons. This data frame has to contain a gene_id column with gene IDs, feature_id column with feature IDs and columns with counts for each sample. Column names corresponding to sample IDs must be the same as in the sample data frame.
samples	Data frame where each row corresponds to one sample. Columns have to contain unique sample IDs in sample_id variable and a grouping variable group.

Value

Returns a dmDSdata object.

Author(s)

Malgorzata Nowicka

See Also

plotData

Examples

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

library(PasillaTranscriptExpr)

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

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

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

## Create a pasilla_samples data frame
pasilla_samples <- data.frame(sample_id = pasilla_metadata$SampleName, 
  group = pasilla_metadata$condition)
levels(pasilla_samples$group)

## Create a dmDSdata object
d <- dmDSdata(counts = pasilla_counts, samples = pasilla_samples)

## 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, ]

gosianow/DRIMSeq documentation built on Aug. 8, 2020, 10:29 a.m.