Checks if object is an sq object
without specifying type or if it is an sq object with specific type.
is.sq(x)
is.sq_dna_bsc(x)
is.sq_dna_ext(x)
is.sq_dna(x)
is.sq_rna_bsc(x)
is.sq_rna_ext(x)
is.sq_rna(x)
is.sq_ami_bsc(x)
is.sq_ami_ext(x)
is.sq_ami(x)
is.sq_unt(x)
is.sq_atp(x)[sq]
An object this function is applied to.
A logical value - TRUE if x has specified type,
FALSE otherwise.
These functions are mostly simply calls to class checks. There are also
grouped checks, i.e. is.sq_dna, is.sq_rna and is.sq_ami.
These check for sq type regardless of if the type is basic or extended.
Functions that manipulate type of sequences:
find_invalid_letters(),
sq_type(),
substitute_letters(),
typify()
Functions from utility module:
==.sq(),
get_sq_lengths(),
sqconcatenate,
sqextract
# Creating objects to work on:
sq_dna <- sq(c("GGCAT", "TATC-A", "TGA"), alphabet = "dna_bsc")
sq_rna <- sq(c("CGAUUACG", "UUCUAGA", "UUCA"), alphabet = "rna_bsc")
sq_ami <- sq(c("CVMPQGQQ", "AHLC--PPQ"), alphabet = "ami_ext")
sq_unt <- sq("BAHHAJJ&HAN&JD&", alphabet = "unt")
sq_atp <- sq(c("mALPVQAmAmA", "mAmAPQ"), alphabet = c("mA", LETTERS))
# What is considered sq:
is.sq(sq_dna)
#> [1] TRUE
is.sq(sq_rna)
#> [1] TRUE
is.sq(sq_ami)
#> [1] TRUE
is.sq(sq_unt)
#> [1] TRUE
is.sq(sq_atp)
#> [1] TRUE
# What is not:
is.sq(c(1,2,3))
#> [1] FALSE
is.sq(LETTERS)
#> [1] FALSE
is.sq(TRUE)
#> [1] FALSE
is.sq(NULL)
#> [1] FALSE
# Checking for exact class:
is.sq_dna_bsc(sq_dna)
#> [1] TRUE
is.sq_dna_ext(sq_rna)
#> [1] FALSE
is.sq_rna_bsc(sq_ami)
#> [1] FALSE
is.sq_rna_ext(sq_rna)
#> [1] FALSE
is.sq_ami_bsc(sq_ami)
#> [1] FALSE
is.sq_ami_ext(sq_atp)
#> [1] FALSE
is.sq_atp(sq_atp)
#> [1] TRUE
is.sq_unt(sq_unt)
#> [1] TRUE
# Checking for generalized type:
is.sq_dna(sq_atp)
#> [1] FALSE
is.sq_rna(sq_rna)
#> [1] TRUE
is.sq_ami(sq_ami)
#> [1] TRUE