check_filter: Check and filter valid base of nucleotide sequences

Description Usage Arguments Value Author(s) Examples

View source: R/check_filter.R

Description

In general, whitespaces and non-base characters are removed and characters are converted to uppercase in given method.

Usage

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check_filter(ntseq, method)

Arguments

ntseq

The primer/probe sequence as string or vector of characters

method

TM_Wallace: check and return "A","B","C","D","G","H","I","K","M","N","R","S","T","V","W" and "Y"

TM_GC: check and return "A","B","C","D","G","H","I","K","M","N","R","S","T","V","W", "X" and "Y"

TM_NN: check and return "A","C","G","I" and "T"

Value

Return a sequence which fullfils the requirements of the given method.

Author(s)

Junhui Li

Examples

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ntseq <- c("ATCGBDHKMNRVYWSqq")
check_filter(ntseq,method='Tm_Wallace')
check_filter(ntseq,method='Tm_NN')

TmCalculator documentation built on May 2, 2019, 6:04 a.m.