example.seasnake: Example SEAsnake outputs

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

Example SEAsnake outputs

Description

A list contains SEAsnake results including gene counts, library quality metrics, and sample metadata.

Usage

example.seasnake

Format

Class 'list' with 5 slots:

1. fcounts A data frame with 19118 rows and 13 columns

   Geneid

   character. ENSEMBL gene ID.

   lib1

   numeric. Counts in library 1.

   lib2

   numeric. Counts in library 2.

   lib3

   numeric. Counts in library 3.

   lib4

   numeric. Counts in library 4.

   lib5

   numeric. Counts in library 5.

   lib6

   numeric. Counts in library 6.

   lib7

   numeric. Counts in library 7.

   lib8

   numeric. Counts in library 8.

   lib9

   numeric. Counts in library 9.

   lib10

   numeric. Counts in library 10.

   lib11

   numeric. Counts in library 11.

   lib12

   numeric. Counts in library 12.

2. flagstat A data frame with 12 rows and 17 columns

   See http://www.htslib.org/doc/samtools-flagstat.html

3. picard A data frame with 12 rows and 31 columns

   See http://broadinstitute.github.io/picard/picard-metric-definitions.html#RnaSeqMetrics

4. patient A data frame with 5 rows and 4 columns

   ptID

   character. patient ID.

   asthma

   character. Patient classification as healthy or asthma.

   age

   numeric. Patient age in years.

   sex

   character. Patient biological sex: male or female.

5. sample A data frame with 12 rows and 4 columns

   libID

   character. Libray ID.

   ptID

   character. Patient ID.

   virus

   character. Sample treatment: media control (none) or human rhinovirus infected (HRV).

   batch

   character. Sequenceing batch: A or B.

Source

https://github.com/BIGslu/SEAsnake

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.