miR_converter {anamiR} | R Documentation |
This function will convert the miRNA names from the data frame, which is produced by differExp_discrete, to the miRBase 21 version of miRNA annotation. If the input contains hundreds of miRNAs, it would take a few minutes to convert all of them.
miR_converter(data, remove_old = TRUE, original_version, latest_version = 21)
data |
expression data in data.frame format, with sample name in columns and miRNA name in rows. |
remove_old |
logical value, if the miRNA is deleted in miRBase 21, should it be removed from row? Default is TRUE. |
original_version |
the original version of miRNA in input matrix. This one is necessary. |
latest_version |
choose an interger under 21, and this function would convert miRNA annotation to that version. Default is 21. |
expression data in data.frame format, with sample name in columns and miRNA name for miRBase version 21 in rows.
## Use the internal dataset data("mirna", package = "anamiR", envir = environment()) data("pheno.mirna", package = "anamiR", envir = environment()) ## SummarizedExperiment class require(SummarizedExperiment) mirna_se <- SummarizedExperiment( assays = SimpleList(counts=mirna), colData = pheno.mirna) ## Finding differential miRNA from miRNA expression data with t.test mirna_d <- differExp_discrete( se = mirna_se, class = "ER", method = "t.test" ) ## Convert annotation to miRBse 21 mirna_21 <- miR_converter(data = mirna_d, original_version = 17)