farrisTxSE: Farris et al transcript-level expression data

In jmw86069/farrisdata: Farris et al 2019, mouse hippocampus RNA-seq data objects

Farris et al transcript-level expression data

Description

Farris et al transcript-level expression data

Usage

farrisTxSE

Format

SummarizedExperiment object with 122733 transcript rows, and 24 sample columns. Sample annotations are accessed as described for SummarizedExperiment-class objects, using SummarizedExperiment::colData(). Transcript and gene annotations are accessed using SummarizedExperiment::rowData().

The colData colnames are described as follows:

CellType

The major excitatory pyramidal cell types in the mouse hippocampus, CA1, CA2, CA3, and dentate gyrus (DG).

Compartment

The cellular compartment within each cell type: CB (cell body) is the pyramidal cell layer; DE (dendrite) is stratum radiatum of CA1, CA2, CA3, and the molecular layer of DG.

AnimalID

The number assigned to each mouse.

groupName

The sample group name associated with each CellType and Compartment.

The count data is accessed through the function assays and has the following entries:

tpm

Median-normalized log2-transformed TPM values generated by Salmon, after import using tximport::tximport(). The log2 transformation was log2(1+x).

counts

Median-normalized log2-transformed pseudocount data per-gene generated by Salmon, after import using tximport::tximport(). The log2 transformation was log2(1+x).

raw_tpm

Raw log2-transformed TPM values generated by Salmon, after import using tximport::tximport(). The log2 transformation was log2(1+x).

raw_counts

The raw log2-transformed pseudocount data per-gene generated by Salmon. The log2 transformation was log2(1+x).

The rowData contains gene annotations, which includes the relationship between transcript and gene.

transcript_id

Gencode transcript_id as defined in the GTF file.

geneSymbol

Most current Entrez gene symbol associated with the transcript_id, as of June 2018.

gene_type,transcript_type

Gencode attributes as defined in the GTF file.

has3UTR,TxHas3UTR

Boolean indicating whether the gene or transcript contained an annotated 3'UTR region defined in the Gencode GTF file.

TxHasExt3UTR,GeneHasExt3UTR

Following 3'UTR extension based upon RNA-seq data coverage, this boolean field indicates whether each transcript or gene contains a 3'UTR with or without extension by observed RNA-seq coverage.

TxDetectedByTPM

Boolean indicating whether each transcript was considered "detected" based upon TPM and count data per gene, as described in splicejam::defineDetectedTx().

Details

SummarizedExperiment object containing transcript-level expression data following Salmon quantitation, and import using tximport::tximport() at the transcript level. Data is stored as log2-transformed TPM, and log2-transformed pseudocounts from Salmon, after median normalization.

Source

Farris et al publication.

See Also

Other farrisdata SummarizedExperiment data: farrisGeneSE, farrisdata

Examples

data(farrisTxSE);
## Transcript-Gene annotation DataFrame
if (suppressPackageStartupMessages(require(knitr))) {
   knitr::kable(
      tail(head(SummarizedExperiment::rowData(farrisTxSE), 15385), 10)
   )
} else {
   tail(head(SummarizedExperiment::rowData(farrisTxSE), 15385), 10)
}

## Sample annotation DataFrame
if (suppressPackageStartupMessages(require(knitr))) {
   knitr::kable(
      SummarizedExperiment::colData(farrisTxSE)
   )
} else {
   head(SummarizedExperiment::colData(farrisTxSE));
}

## Assay data matrix for normalized TPM
if (suppressPackageStartupMessages(require(knitr))) {
   knitr::kable(
      tail(head(SummarizedExperiment::assays(farrisTxSE)[["tpm"]], 15385), 10)
   )
} else {
   tail(head(SummarizedExperiment::assays(farrisTxSE)[["tpm"]], 15385), 10)
}

jmw86069/farrisdata documentation built on Oct. 14, 2024, 6:29 p.m.