example.dat: kimma example DGEList.

In BIGslu/kimma: Kinship In Mixed Model Analysis of RNA-seq

kimma example DGEList.

Description

An edgeR DGEList data set containing unnormalized RNA-seq counts. RNA-seq of human dendritic cells cultured with and without virus. Samples from 3 donors and a random subset of 1000 genes were selected. Counts are unnormalized.

Usage

example.dat

Format

Formal class 'DGEList' [package "edgeR"] with 1 slot:

1. counts A matrix with 1000 rows and 12 columns

   rownames

   character. ENSEMBL gene ID.

   lib1

   integer. Counts in library 1.

   lib2

   integer. Counts in library 2.

   lib3

   integer. Counts in library 3.

   lib4

   integer. Counts in library 4.

   lib5

   integer. Counts in library 5.

   lib6

   integer. Counts in library 6.

   lib7

   integer. Counts in library 7.

   lib8

   integer. Counts in library 8.

   lib9

   integer. Counts in library 9.

   lib10

   integer. Counts in library 10.

   lib11

   integer. Counts in library 11.

   lib12

   integer. Counts in library 12.

2. samples A data frame with 12 rows and 9 columns

   group

   factor. No grouping was provided. All = 1.

   lib.size

   numeric. Total library size for this 1000 gene subset.

   norm.factors

   numeric. Normalizatin factors. No normalization was completed. All = 1.

   libID

   character. Unique library ID. Matches column names in counts.

   donorID

   character. Donor ID.

   median_cv_coverage

   numeric. Median coefficient of variation of coverage. Quality metric for sequencing libraries calculated from original full data set.

   virus

   Factor. Media samples with no virus ("none") vs virus-infected samples ("HRV").

   asthma

   Factor. Asthma vs healthy.

3. genes A data frame with 1000 rows and 5 columns

   hgnc_symbol

   character. Current approved HGNC symbol.

   Previous symbols

   character. Previous HGNC symbols.

   Alias symbols

   character. Alias HGNC symbols.

   gene_biotype

   character. Gene product type. All = protein-coding.

   geneName

   character. ENSEMBL gene ID. Matches row names in counts.

Source

https://github.com/altman-lab/P259_pDC_public

References

Dill-McFarland et al. 2022 Eosinophil-mediated suppression and Anti-IL-5 enhancement of plasmacytoid dendritic cell interferon responses in asthma. J Allergy Clin Immunol. 150(3):666-675. doi: 10.1016/j.jaci.2022.03.025

BIGslu/kimma documentation built on May 30, 2024, 10:09 p.m.