indel_info: A data set for indel information.

In chandlerzuo/atIndel: Affinity test for identifying regularity Indels

A data set for indel information.

Description

This is a list object loaded by 'data(example)'. Each element corresponds to an indel and includes the following components:

inserted_sequence	An integer vector representing the deroxyribose sequence around each indel location for the longer sequence. For an insertion, this is the inserted sequence. For an deletion, this is the reference allele sequence. Nucleotides are coded as "A"-1, "C"-2, "G"-3, "T"-4.
insertion_len	The length of the inserted / deleted sequence.
insertion	A boolean variable indicating whether the indel is an insertion (TRUE) or a deletion (FALSE).
ref	A character vector for the nucleotides around the indel location on the reference allele. For deletion, this is the nucleotide before the deletion location plus the deleted nucleotides. For insertion, this is the nucleotide before the insertion location.
alt	A character vector for the nucleotides around the indel location on the alternative allele. For insertion, this is the nucleotide before the insertion location plus the inserted nucleotides. For deletion, this is the nucleotide before the deletion location.

Format

A list object.

Author(s)

Qinyi Zhou [e-mail], Chandler Zuo [e-mail], Sunyoung Shin [e-mail]

chandlerzuo/atIndel documentation built on Jan. 20, 2024, 4:10 a.m.