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ID transform SE or DEGdata

ID_transform.Rd

Transform ID for SummarizedExperiment or DEGdata according origin ID. The annotation package of certain species must be installed. Using annoSpecies_df to check species names and the required packages.

Usage

ID_transform(
  x,
  from_columns = "rownames",
  fromtype = "ENSEMBL",
  species = "Human",
  replace_rowname = "SYMBOL"
)

Arguments

x

SummarizedExperiment object from make_se()) or make_pe()), or a DEGdata object from test_diff_deg()).

from_columns

Character(), the origin ID from one of "rownames" or column of rowData(x)

fromtype

Character(1), the type of origin ID, e.g. "ENSEMBEL", "SYMBOL", "UNIPROT", "ENTREZID".

species

Character(1), the species name.

replace_rowname

NULL or character. Should be one of NULL, "SYMBOL", "ENTREZID", "UNIPROT", "ENSEMBL". If it is not NULL, replace rownames(x) by selected kind of ID.

Value

A SummarizedExperiment or DEGdata which rowData includes gene information like "ENSEMBEL", "SYMBOL", "UNIPROT" or "ENTREZID" transformed from giving ID. If x is a DEGdata, gene information table is also store in the geneinfo slot. Rownames of object are replaced according replace_rowname.

Examples

if (FALSE) {
data(Silicosis_pg)
data <- Silicosis_pg
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")
ecols <- grep("LFQ.", colnames(data_unique))
se <- make_se_parse(data_unique, ecols,mode = "delim")

## transform uniport ID
check_organismDB_depends(organism = "Mouse") # check annotation package of Mouse
head(rowData(se)$ID)
se2 <- ID_transform(se,from_columns = "ID",fromtype = "UNIPROT",species = "Mouse")
head(rowData(se2)$SYMBOL)
head(rownames(se2))
}