tidysq (version 1.2.3)

is_empty_sq: Test if sequence is empty

Description

Test an sq object for presence of empty sequences.

Usage

is_empty_sq(x)
# S3 method for sq
is_empty_sq(x)

Value

A logical vector of the same length as input sq, indicating whether elements are empty sequences (of length 0).

Arguments

x

[sq]
An object this function is applied to.

Details

This function allows identification of empty sequences (that have length 0) represented by the NULL sq values in the sq object. It returns a logical value for every element of the sq object - TRUE if its value is NULL sq and FALSE otherwise. NULL sq values may be introduced as a result of remove_ambiguous and remove_na functions. The former replaces sequences containing ambiguous elements with NULL sq values, whereas the latter replaces sequences with NA values with NULL sq.

See Also

sq class

Functions that clean sequences: remove_ambiguous(), remove_na()

Examples

# Creating an object to work on:
sq_dna_ext <- sq(c("ACGATTAGACG", "", "GACGANTCCAGNTAC"),
                 alphabet = "dna_ext")

# Testing for presence of empty sequences:
is_empty_sq(sq_dna_ext)

# Testing for presence of empty sequences after cleaning - sequence
# containing ambiguous elements is replaced by NULL sq:
sq_dna_bsc <- remove_ambiguous(sq_dna_ext)
is_empty_sq(sq_dna_bsc)

# Testing for presence of empty sequences after using bite and removing NA.
# Extracting letters from first to fifteenth - NA introduced:
bitten_sq <- bite(sq_dna_ext, 1:15)
# Removing NA:
rm_bitten_sq <- remove_na(bitten_sq)
# Testing for presence of empty sequences:
is_empty_sq(rm_bitten_sq)