is_empty_sq: Test if sequence is empty

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

Test if sequence is empty

Description

Test an sq object for presence of empty sequences.

Usage

is_empty_sq(x)

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

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.

Value

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

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)

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