Description Usage Arguments Value Examples
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.
1 2 | 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ## 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)
|
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