dmSQTLdata-class: dmSQTLdata object

Description

dmSQTLdata contains genomic feature expression (counts), genotypes and sample information needed for the sQTL analysis. It can be created with function dmSQTLdataFromRanges or dmSQTLdata.

Usage

"names"(x)
"length"(x)
"["(x, i, j)

Arguments

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 contains unique sample names sample_id.

Examples

Run this code

#############################
### sQTL analysis
#############################

d <- data_dmSQTLdata

head(names(d))
length(d)
d[1:10, ]
d[1:10, 1:10]