Pre-process a gene expression matrix to have different gene annotation
Source:R/gexp_preprocess.R
gexp_preprocess.RdPre-process a gene expression matrix to have different gene annotation
Usage
gexp_preprocess(
gexp,
gene_annotation = NULL,
keep_annot = "gene_name",
og_annot = "gene_id",
keep_stat = sum
)Arguments
- gexp
A gene expression matrix, with samples in columns and genes in rows
- gene_annotation
A data.frame of gene annotation, refering to the rows of `gexp`. It must contain at least two columns: one for the `keep_annot` and one for the `og_annot`
- keep_annot
The name of the column in `gene_annotation` that contains the gene names that you would like to put as rownames of your `gexp`, i.e. the kept annotation
- og_annot
The name of the column in `gene_annotation` that contains the gene names currently being used by `gexp`, i.e. the original annotation.
- keep_stat
a function for the statistical measure used for keeping a gene when `keep_annot` doesn't map uniquely to `og_annot`.