example.voom: kimma example EList.

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

kimma example EList.

Description

A limma EList data set containing normalized log2 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 TMM normalized log2 counts per million (CPM).

Usage

example.voom

Format

Formal class 'EList' [package "limma"] with 1 slot:

1. 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 E.

2. targets A data frame with 12 rows and 8 columns

   group

   factor. No grouping was provided. All = 1.

   lib.size

   numeric. Total library size for this 1000 gene subset.

   norm.factors

   numeric. TMM normalizatin factors.

   libID

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

   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. E A matrix with 1000 rows and 12 columns

   rownames

   character. ENSEMBL gene ID.

   lib1

   numeric. log2 CPM in library 1.

   lib2

   numeric. log2 CPM in library 2.

   lib3

   numeric. log2 CPM in library 3.

   lib4

   numeric. log2 CPM in library 4.

   lib5

   numeric. log2 CPM in library 5.

   lib6

   numeric. log2 CPM in library 6.

   lib7

   numeric. log2 CPM in library 7.

   lib8

   numeric. log2 CPM in library 8.

   lib9

   numeric. log2 CPM in library 9.

   lib10

   numeric. log2 CPM in library 10.

   lib11

   numeric. log2 CPM in library 11.

   lib12

   numeric. log2 CPM in library 12.

4. weights A matrix with 1000 rows and 6 columns

   1

   numeric. limma gene weights for library 1.

   2

   numeric. limma gene weights for library 2.

   3

   numeric. limma gene weights for library 3.

   4

   numeric. limma gene weights for library 4.

   5

   numeric. limma gene weights for library 5.

   6

   numeric. limma gene weights for library 6.

5. design A matrix with 6 rows and 1 column

   GrandMean

   numeric. limma default design matrix.

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.