check_filter {TmCalculator}

Check and filter invalid base of nucleotide sequences

Description

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

Usage

check_filter(ntseq, method)

Arguments

ntseq

Sequence (5' to 3') of one strand of the DNA nucleic acid duplex 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

References

citation("TmCalculator")

Examples

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