readseq

character, a FASTA data file name with full path.

dataFile

character, 'protein' by default, the type of data will be processed. It could be 'DNA', 'RNA', 'protein', 'SNP' or 'other'.

dataType

logic, FALSE by default, to indicate whether the debug message will be displayed or not.

debug


Reading a sequence file in fasta format


Read and preprocess fasta format data, and construct the co-occurrence network for downstream analyses. This R package is to construct the co-occurrence network with the algorithm developed by Du (2008) <DOI:10.1101/gr.6969007>. It could be used to transform the data with high-dimension, such as DNA or protein sequence, into co-occurrence networks. Co-occurrence network could not only capture the co-variation pattern between variables, such as the positions in DNA or protein sequences, but also reflect the relationship between samples. Although it is originally used in DNA and protein sequences, it could be also used to other kinds of data, such as RNA, SNP, etc.

readseq: readseq

Description

Usage

Arguments

Value

Examples