AVARDA_compiled: Primary function to run AVARDA modules together

In drmonaco/AVARDA: AntiViral Antibody Response Deconvolution Algorithm (AVARDA), a multi-module software package for analyzing VirScan datasets

Description

Primary function to run AVARDA modules together

Usage

AVARDA_compiled(
  case_data,
  blast,
  total_prob,
  pairwise,
  dict,
  threshold = 5,
  cores,
  mod_3
)

Arguments

case_data	A data.frame of PhIPseq data that identifies hits by some theshold, can be binary hits or some value
blast	A data.frame listing the blastp, or tblastn, alignments of PhIP-seq peptides to organisms of interact
total_prob	A data.frame listing the degree of representation each virus has in the phip-seq library
pairwise	A number.
dict	A number.
threshold	A number.
cores	A number.
mod_3	A number.

Value

Output of AVARDA algorithm; a data frame listing the likelihood of each virus causing in infection in a given sample

Examples

## Not run: do later

drmonaco/AVARDA documentation built on Dec. 20, 2021, 1:18 a.m.