MIQuerySeq: MIQuerySeq

In brengong/ConservationtextmineR:

Description

Adds a row to the original data.table containing the query sequence of the miRNA. Requires a column named "seed_Sequence" housing the miRNA sequence and a column named "miRNA_Name" housing the name of the miRNA.

Usage

MIQuerySeq(DT, wobble = FALSE)

Arguments

DT	a data table with one column labeled seed_Sequence
wobble	a logical statement either TRUE or FALSE. If wobble = TRUE, will returen a query sequence allowing for G-U basepairing. If wobble = FALSE, will return a query sequence that considers only Watson-Crick base pairing.

Value

A data table containing the following columns:

Author(s)

Brendan Gongol

Examples

Sequence <- c("UGAGGUAGUAGGUUGUAUAGUU", "CUAUGCAUAGCGAUACCUUACC", "UCCCUGAGACCUCAAGUGUGA", "ACACCUGGGCUCUCCGGGUACC",
              "UAGCGAUCCUUACAUGCCCAUA", "UCGUGUCCGUUUCUCGUUUCGA", "ACAAUAAUCGGACACUAGCGAU", "CACACCGGACGAGAUUUCAU",
              "UACCGGGCGUGGGGAGGGCAGG", "UAGCGAUUCCUUCUUAGCGAU")
miRNA_Name <- c("hsa-let-7","cel-lin-4","aae-mir-1","bol-mir-2","rno-mir-34",
                "cel-lin-4-5p", "ame-miR-9895", "rno-miR-3478", "mmu-miR9897-5p", "cre-miR9897-3p")
miRNA_type <- c("MATURE", "MATURE", "MATURE", "MATURE", "MATURE",
                "MATURE", "MATURE", "MATURE", "MATURE", "MATURE")
seed_Sequence <- c("GAGGUAG", "UAUGCAU", "CCCUGAG", "CACCUGG", "AGCGAUC",
                   "CGUGUCC", "CAAUAAU", "ACACCGG", "ACCGGGC", "AGCGAUU")
MiRNADT<- data.frame(cbind(Sequence, miRNA_Name, miRNA_type, seed_Sequence))
MiRNADT$Sequence <- as.character(MiRNADT$Sequence)
MiRNADT$seed_Sequence <- as.character(MiRNADT$seed_Sequence)
MIQuerySeq(MiRNADT)

brengong/ConservationtextmineR documentation built on July 29, 2019, 10:05 a.m.