equals-.sq: Compare sq objects

In tidysq: Tidy Processing and Analysis of Biological Sequences

Compare sq objects

Description

Compares input sq object with either another sq object or character vector.

Usage

## S3 method for class 'sq'
e1 == e2

Arguments

e1	[sq] An object this comparison is applied to.
e2	[sq || character] An object to compare with x1.

Details

`==` compares compatible object for equality of their respective sequences. Objects are considered compatible, when either both have same length or one of them is a scalar value (i.e. a vector of length 1). Moreover, not every e1 sq type can be compared to any e2 sq type.

To see which types are compatible, see Details of sq-concatenate.

`==` returns logical vector, where each element describes whether elements at position n of both e1 and e2 are equal in meaning (that is, they may be represented differently, but their biological interpretation must be identical). If one of compared objects is a scalar, then said logical vector describes comparison for each element of the other, longer vector.

Value

A logical vector indicating on which positions these objects are equal.

See Also

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

Examples

# Creating objects to work on:
sq_dna_1 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"),
               alphabet = "dna_bsc")
sq_dna_2 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"),
               alphabet = "dna_bsc")
sq_dna_3 <- sq(c("ACTGCTG", "CTTAGA", "GGAA"),
               alphabet = "dna_bsc")
sq_dna_4 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "GTNANN"),
               alphabet = "dna_ext")
sq_ami_1 <- sq(c("ACTGCTG", "NIKAAR", "CCCT", "CTGAATGT"),
               alphabet = "ami_bsc")
sq_unt <- sq(c("AHSNLVSCTK$SH%&VS", "YQTVKA&#BSKJGY",
               "CCCT", "AVYI#VSV&*DVGDJCFA"))

# Comparing sq object with an object of the same length:
sq_dna_1 == sq_dna_2
sq_dna_1 == c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT")

# Cannot compare sq objects of different lengths:
## Not run: 
sq_dna_1 == sq_dna_3
sq_dna_1 == c("AAA", "CCC")

## End(Not run)

# Unless comparing sq object with scalar value:
sq_dna_1 == "CTTAGA"

# It's possible to compare basic and extended types:
sq_dna_1 == sq_dna_4

# Mixing DNA, RNA and amino acid types throws an error, however:
## Not run: 
sq_dna_1 == sq_ami_1

## End(Not run)

# On the other hand, unt sq is acceptable everywhere:
sq_dna_1 == sq_unt
sq_dna_4 == sq_unt
sq_ami_1 == sq_unt

tidysq documentation built on April 12, 2025, 1:37 a.m.