Expression-class: An S4 class to represent gene expression data for multiple...
In caseywdunn/agalmar: A Collection of Tools for Analyzing Agalma Expression Projects

The fields that apply to the s samples correspond to those

species: The species
edgeR: An edgeR DGEList object holding data for all samples. Expression matrix of dimension g,s.
lengths: Summary of length, in bp, of transctipts for each gene. Length g.
individual: Factors indicating which individual each sample is from. Length s.
treatment: Factors indicating which treatment applies to each sample. Length s.
id: Factors indicating the unique sequencing run id of each sample, eg HWI-ST625-75-D0PBDACXX-6-ATCACG. Length s.
library_id: Factors indicating the unique library id of each sample, eg FEG365. Length s.
sample_prep: Sample prep strategy. Length s.
genome_type: Character indicating genome type, eg nuclear. See agalma documentation. Length g.
molecule_type: Character indicating encoded molecule type, eg protein. See agalma documentation. Length g.
blast_hit: Blast hit. Length g.
rRNA: Fraction of reads in sample that are rRNA. Length s.
protein: Fraction of reads in sample that are protein coding. Length s.
x: The counts matrix

caseywdunn/agalmar documentation built on May 13, 2019, 1:11 p.m.

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