ap_aaindex: Find amino acid indices

In cekehe/rappp: QC, data transformation and visualization for PAPP

Find amino acid indices

Description

Align query sequnces to full length sequences to find start and stopp indices of sequences.

Usage

ap_aaindex(x, fasta_list = NULL, sequence_list = NULL)

Arguments

x	List with at least one element, see Deatils for naming and content.
fasta_list	A list of sequences in fasta format. Either this or sequence_list should be provided.
sequence_list	A list of only sequences. Either this or fasta_list should be provided.

Details

NB! The sequences have to be identical matches to consequtive stretches in the full length sequence you are aligning to. A future update will include partial matches.

The x list needs to include at least the element

BEADS = Beads info with identifiable rownames and with at least the columns:

"Sequence" with one letter abriviation for the aminoa acids,

"Uniprot" withthe uniprot ID the sequence originates from

If a list of fasta sequences is provided (fasta_list), it should be the output of read.fasta() in the package seqinr.

If a list of only sequenes is provided (sequence_list), each element should correspond to a Uniprot ID, isoform specific if applicable, and contain a consequitive string of one letter amino acid abbreviations.

Value

Updated input x with new columns in the BEADS element for the start and stopp indices of each tested isoform.

cekehe/rappp documentation built on May 17, 2022, 8:54 a.m.