check_ogset: Check Validity of an 'ogset' class element

In OthoMantegazza/crossr: Functions For Cross Species Quantitative Transcriptomics

Check Validity of an ogset class element

Description

The function check_ogset checks that in the provided object:

• the names of the orthogroups (og) match the rownames of the orthogroup expression set og_eset (if any is given),

• the row names of og_annos are contained in the names of the orthogroup list

• the row names of colData (if any) match the column names of the orthogroup expression set og_eset,

• the row names of rowData (if any) match the row names of the orthogroup expression set og_eset,

• the variable in design (if any) are colnames of colData,

• the rownames of spec1_colData match the colnames spec1_exp (if any),

• the rownames of spec2_colData match the colnames spec2_exp (if any),

• exp_cond is a character string

• exp_cond is contained in columns of spec1_colData and spec2_colData and that those columns match.

Usage

check_ogset(object)

Arguments

object

an ogset class element

OthoMantegazza/crossr documentation built on Feb. 1, 2023, 4:15 a.m.