remove_na: Remove sequences that contain NA values

In tidysq: Tidy Processing and Analysis of Biological Sequences

Remove sequences that contain NA values

Description

This function replaces sequences with NA values by empty (NULL) sequences or removes NA values from sequences in an sq object.

Usage

remove_na(x, by_letter = FALSE, ...)

## S3 method for class 'sq'
remove_na(x, by_letter = FALSE, ..., NA_letter = getOption("tidysq_NA_letter"))

Arguments

x	[sq] An object this function is applied to.
by_letter	[logical(1)] If FALSE, filter condition is applied to sequence as a whole. If TRUE, each letter is applied filter to separately.
...	further arguments to be passed from or to other methods.
NA_letter	[character(1)] A string that is used to interpret and display NA value in the context of sq class. Default value equals to "!".

Details

NA may be introduced as a result of using functions like substitute_letters or bite. They can also appear in sequences if the user reads FASTA file using read_fasta or constructs sq object from character vector with sq function without safe_mode turned on - and there are letters in file or strings other than specified in the alphabet.

remove_na() is used to filter out sequences or elements that have NA value(s). By default, if any letter in a sequence is NA, then whole sequence is replaced by empty (NULL) sequence. However, if by_letter parameter is set to TRUE, then sequences are only shortened by excluding NA values.

Value

An sq object with the same type as the input type. Sequences that do not contain any NA values are left unchanged.

See Also

sq

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

Examples

# Creating objects to work on:
sq_ami <- sq(c("MIAANYTWIL","TIAALGNIIYRAIE", "NYERTGHLI", "MAYXXXIALN"),
             alphabet = "ami_ext")
sq_dna <- sq(c("ATGCAGGA", "GACCGAACGAN", "TGACGAGCTTA", "ACTNNAGCN"),
             alphabet = "dna_ext")

# Substituting some letters with NA
sq_ami_sub <- substitute_letters(sq_ami, c(E = NA_character_, R = NA_character_))
sq_dna_sub <- substitute_letters(sq_dna, c(N = NA_character_))

# Biting sequences out of range
sq_bitten <- bite(sq_ami, 1:15)

# Printing the sequences
sq_ami_sub
sq_dna_sub

# Removing sequences containing NA
remove_na(sq_ami_sub)
remove_na(sq_dna_sub)
remove_na(sq_bitten)

# Removing only NA elements
remove_na(sq_ami_sub, by_letter = TRUE)
remove_na(sq_dna_sub, TRUE)
remove_na(sq_bitten, TRUE)

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