check_gene_df_type {orthogene} | R Documentation

## Check gene_df

### Description

Handles gene_df regardless of whether it's a data.frame, matrix, list, or vector

### Usage

    check_gene_df_type(gene_df, gene_input, verbose = TRUE)

### Arguments

`gene_df` | Data object containing the genes (see `gene_input` for options on how the genes can be stored within the object). Can be one of the following formats: `matrix` : A sparse or dense matrix. `data.frame` : A `data.frame`, `data.table`. or `tibble`. codelist : A `list` or character `vector`. Genes, transcripts, proteins, SNPs, or genomic ranges can be provided in any format (HGNC, Ensembl, RefSeq, UniProt, etc.) and will be automatically converted to gene symbols unless specified otherwise with the `...` arguments. Note: If you set `method="homologene"`, you must either supply genes in gene symbol format (e.g. "Sox2") OR set `standardise_genes=TRUE`.
`gene_input` | Which aspect of `gene_df` to get gene names from: `"rownames"` : From row names of data.frame/matrix. `"colnames"` : From column names of data.frame/matrix. `<column name>` : From a column in `gene_df`, e.g. `"gene_names"`.
`verbose` | Print messages.

### Value

List of gene_df and gene_input

[Package orthogene version 1.0.2 Index]