findpos: 'Find SNP Position'

Description Usage Arguments Value Examples

Description

Find the physical position of a short sequence in a given genome.

Usage

1
findpos(blastbin = NULL, db, fa, iden, len)

Arguments

blastbin

The path of binary code for NCBI BLAST program. [String, default=NULL]

db

Path of database to BLAST against. [String]

fa

A fasta file of the sequences of interest. [String]

iden

Percent identity of the alignment. [interger, default=95]

len

Minimum length of the alignment. [interger, default=100]

Value

return a data.frame.

Examples

1
2
3
4
5
6
7
8
library("Biostrings")
library("findpos")
### Find the help document for the function
?findpos
### run
 res <- findpos(blastbin = "~/bin/ncbi-blast-2.4.0+/bin",
                db="example/16SMicrobialDB/16SMicrobial",
                fa="example/rna.fasta", iden=95, len=100)

yangjl/findpos documentation built on May 4, 2019, 2:28 p.m.