dmSQTLdata-class: dmSQTLdata object

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

Description

dmSQTLdata contains genomic feature expression (counts), genotypes and sample information needed for the transcript/exon usage QTL analysis. It can be created with function dmSQTLdata.

Usage

## S4 method for signature 'dmSQTLdata'
counts(object)

## S4 method for signature 'dmSQTLdata'
samples(x)

## S4 method for signature 'dmSQTLdata'
names(x)

## S4 method for signature 'dmSQTLdata'
length(x)

## S4 method for signature 'dmSQTLdata,ANY'
x[i, j]

Arguments

x, object	dmSQTLdata object.
i, j	Parameters used for subsetting.

Value

• names(x): Get the gene names.

• length(x): Get the number of genes.

• x[i, j]: Get a subset of dmDSdata object that consists of counts, genotypes and blocks corresponding to genes i and samples j.

Slots

counts

MatrixList of expression, in counts, of genomic features. Rows correspond to genomic features, such as exons or transcripts. Columns correspond to samples. MatrixList is partitioned in a way that each of the matrices in a list contains counts for a single gene.

genotypes

MatrixList of unique genotypes. Rows correspond to blocks, columns to samples. Each matrix in this list is a collection of unique genotypes that are matched with a given gene.

blocks

MatrixList with two columns block_id and snp_id. For each gene, it identifies SNPs with identical genotypes across the samples and assigns them to blocks.

samples

Data frame with information about samples. It must contain variable sample_id with unique sample names.

Author(s)

Malgorzata Nowicka

See Also

dmSQTLprecision, dmSQTLfit, dmSQTLtest

Examples

# --------------------------------------------------------------------------
# Create dmSQTLdata object
# --------------------------------------------------------------------------
# Use subsets of data defined in the GeuvadisTranscriptExpr package

library(GeuvadisTranscriptExpr)

geuv_counts <- GeuvadisTranscriptExpr::counts
geuv_genotypes <- GeuvadisTranscriptExpr::genotypes
geuv_gene_ranges <- GeuvadisTranscriptExpr::gene_ranges
geuv_snp_ranges <- GeuvadisTranscriptExpr::snp_ranges

colnames(geuv_counts)[c(1,2)] <- c("feature_id", "gene_id")
colnames(geuv_genotypes)[4] <- "snp_id"
geuv_samples <- data.frame(sample_id = colnames(geuv_counts)[-c(1,2)])

d <- dmSQTLdata(counts = geuv_counts, gene_ranges = geuv_gene_ranges,  
  genotypes = geuv_genotypes, snp_ranges = geuv_snp_ranges, 
  samples = geuv_samples, window = 5e3)

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