Usage
getSeedMatrix(mRNA, miRNA, species = "human",
id_type = "ensembl_transcript_id", mRNA_id_type = id_type,
miRNA_id_type = id_type, longest3utr = TRUE,
biomart = "ensembl", dataset = "hsapiens_gene_ensembl",
returnGeneInfo = FALSE, convert2genesymbol = TRUE, ...)
Arguments
mRNA
A character vector of N mRNA ids.
miRNA
A character vector of M miRNA ids
species
Common names for a species. Currently only human and mouse are supported as precompiled target site information.
id_type
A string specifying the id type used for both the mRNAs and miRNA.
mRNA_id_type
A string specifying the id type used for the mRNAs.
miRNA_id_type
A string specifying the id type used for the miRNAs.
longest3utr
For genes having multiple transcripts, whetehr to use only the transcript with the longest 3'UTR (default: TRUE).
biomart
Database for biomart, which is ued to obtain transcript information using getBM (default: ensembl). dataset
Dataset used to query the biomart database using getBM (default: hsapiens_gene_ensembl). returnGeneInfo
Binary indicator to return gene information besides seed matrix (default: FALSE); if TRUE, then a list containing seed matrix and gene info is return; otherwise just the seed matrix.
convert2genesymbol
Whether to convert id such as ensembl_gene_id to gene symbols as row names of the seed matrix.
...
Paramters passed to getBM.