ogset-class: S4 Class, Container for Ortholog Expression Data

In othomantegazza/crossr: Functions For Cross Species Quantitative Transcriptomics

S4 Class, Container for Ortholog Expression Data

Description

None of the arguments is required to initialize a ogset class element

Arguments

og	A list of orthogroups
og_annos	a data.frame with functional annotations for the orthogroups
og_exp	A orthogroup-wise expression data.frame
rowData	A data.frame containing the row metadata for the orthogroup expression set
colData	A data.frame containing the sample info for 'og_exp'
desing	A formula describing the experimental design
metadata	A list of metadata
stats	A data.frame with output statistics for 'og_exp'
spec1_exp	A data.frame with expression data for species 1
spec2_exp	A data.frame with expression data for species 2
spec1_colData	A data.frame with sample info for 'spec1_exp'
spec2_colData	A data.frame with sample info for 'spec2_exp'
exp_cond	A character string indicating which variable of 'design' represents the experimental condition under which the two species are compared
og_nomatch	orthogroup represented only in one species, filled by collapse_orthologs

othomantegazza/crossr documentation built on Feb. 1, 2023, 7:44 a.m.