is.sq: Check if object has specified type

In michbur/tidysq: Tidy Processing and Analysis of Biological Sequences

Check if object has specified type

Description

Checks if object is an sq object without specifying type or if it is an sq object with specific type.

Usage

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)

Arguments

x	[sq] An object this function is applied to.

Details

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.

Value

A logical value - TRUE if x has specified type, FALSE otherwise.

See Also

Functions that manipulate type of sequences: find_invalid_letters(), sq_type(), substitute_letters(), typify()

Functions from utility module: ==.sq(), get_sq_lengths(), sqconcatenate, sqextract

Examples

# 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)
is.sq(sq_rna)
is.sq(sq_ami)
is.sq(sq_unt)
is.sq(sq_atp)

# What is not:
is.sq(c(1,2,3))
is.sq(LETTERS)
is.sq(TRUE)
is.sq(NULL)

# Checking for exact class:
is.sq_dna_bsc(sq_dna)
is.sq_dna_ext(sq_rna)
is.sq_rna_bsc(sq_ami)
is.sq_rna_ext(sq_rna)
is.sq_ami_bsc(sq_ami)
is.sq_ami_ext(sq_atp)
is.sq_atp(sq_atp)
is.sq_unt(sq_unt)

# Checking for generalized type:
is.sq_dna(sq_atp)
is.sq_rna(sq_rna)
is.sq_ami(sq_ami)

michbur/tidysq documentation built on April 1, 2022, 5:18 p.m.