README.md

In siyangxia419/virlink: VirScan cross-reactivity and correlation analysis

virlink

A package for analyze of VirScan data for cross-reactivity and co-occurrence

This packages contains functions to calculate pairwise sequence similarity scores and z-score correlations for VirScan profile.

To install this package:

{
if(!require(devtools)) install.packages("devtools")
devtools::install_github(repo = "siyangxia419/virlink", 
                         ref = "main",
                         upgrade = "never")
}

The current version of the pakcage (0.2.1) contains 6 functions:

get_kmer: generate kmers of user-selected length from a longer peptide sequence make_kmer_dataframe: generate a kmer dataset from a peptide dataset using get_kmer peptide_cooccurrence: calculuate a contigency table of two peptide's presence in multiple individuals to_pairwise: given a data frame, perform pairwise analysis with any function on all pairs of columns peptide_pairwise_alignment: perform pairwise sequence alignment for a data frame of peptides, using to_pairwise and pairwiseAlignment in the package "Biostrings" peptide_pairwise_correlation: perform pairwise correlation or co-occurrence analysis for a data frame of peptides, using to_pairwise.

The package also contains two example datasets: peptide_df and peptide_z

siyangxia419/virlink documentation built on Jan. 2, 2022, 12:16 a.m.