remove_nonstandard_aa {ampir}

Remove non standard amino acids from protein sequences

Description

This function removes anything that is not one of the 20 standard amino acids in protein sequences

Usage

remove_nonstandard_aa(df)

Arguments

df

A dataframe which contains protein sequence names as the first column and amino acid sequence as the second column

Value

a dataframe like the input dataframe but with removed proteins that contained non standard amino acids

Examples

non_standard_df <- readRDS(system.file("extdata/non_standard_df.rds", package = "ampir"))

# non_standard_df
#       seq_name            seq_aa
# [1] G1P6H5_MYOLU    MALTVRIQAACLLLLLLASLTSYSLLLSQTTQLADLQTQ....
# [2] fake_sequence   MKVTHEUSYR$GXMBIJIDG*M80-%

remove_nonstandard_aa(non_standard_df)
#       seq_name        seq_aa
# [1] G1P6H5_MYOLU    MALTVRIQAACLLLLLLASLTSYSLLLSQTTQLADLQTQ....