Skip to contents

Splicejam Environment Test Data

Source: R/data-sjenvtest.R
sjenvtest.Rd

Splicejam Environment Test Data, minimal subset of Farris et al bulk RNA-seq data from mouse hippocampus. It contains only 'CellType' values CA1 and CA2, with both 'Compartment' values CB (cell body) and DE (dendrites).

Usage

sjenvtest

Format

environment with components suitable as input to splicejamFigure() and other functions which accept environment as input, typically using argument 'sjenv'.

tx2geneDF

data.frame with colnames including the minimum required: 'gene_name', 'transcript_id'.

detectedGenes

character vector of gene symbols.

detectedTx

character vector of 'transcript_id'.

flatExonsByGene

GRangesList named by 'gene_name'

flatExonsByTx

GRangesList named by 'transcript_id'

txdb

TxDb object used to create various exon GRanges and GRangesList intermediate objects. Not essential for processing, but often useful.

filesDF

data.frame with colnames including the minimum required: 'sample_id', 'url', 'type'

See also

Other Splicejam data: test_cov_gr, test_cov_wide_gr, test_exon_gr, test_exon_wide_gr, test_junc_gr, test_junc_wide_gr