archR

Note: This package is currently under development. So, please bear with me while I put the final blocks together. Thanks for your understanding!

archR is an unsupervised, non-negative matrix factorization (NMF)-based algorithm for discovery of sequence architectures de novo. Below is a schematic of archR’s algorithm.

Installation

Python scikit-learn dependency

This package requires the Python module scikit-learn. See installation instructions here.

To install this package, use

if (!requireNamespace("remotes", quietly = TRUE)) {
    install.packages("remotes")   
}

remotes::install_github("snikumbh/archR", build_vignettes = FALSE)

If the above command produces errors, see this troubleshooting note below.

Usage

# load package
library(archR)
library(Biostrings)


# Creation of one-hot encoded data matrix from FASTA file
# You can use your own FASTA file instead
inputFastaFilename <- system.file("extdata", "example_data.fa", 
                                  package = "archR", 
                                  mustWork = TRUE)

# Specifying dinuc generates dinucleotide features
inputSeqsMat <- archR::prepare_data_from_FASTA(inputFastaFilename,
                                                  sinuc_or_dinuc = "dinuc")

inputSeqsRaw <- archR::prepare_data_from_FASTA(inputFastaFilename, 
                                               raw_seq = TRUE)

nSeqs <- length(inputSeqsRaw)
positions <- seq(1, Biostrings::width(inputSeqsRaw[1]))

# Set archR configuration
# Most arguments have default values
archRconfig <- archR::archR_set_config(
        parallelize = TRUE,
        n_cores = 4,
        n_iterations = 100,
        k_min = 1,
        k_max = 20,
        mod_sel_type = "stability",
        bound = 10^-8,
        inner_chunk_size = 500,
        flags = list(debug = FALSE, time = TRUE, verbose = TRUE,
                     plot = FALSE)

#
### Call/Run archR
archRresult <- archR::archR(config = archRconfig,
                               seqs_ohe_mat = inputSeqsMat,
                               seqs_raw = inputSeqsRaw,
                               seqs_pos = positions,
                               threshold_itr = 2)

Troubleshooting Installation

  1. Error during installation (with remotes::install_github or devtools::install_github. If the error occurs during ** testing if installed package can be loaded, try adding the --no-test-load option as remotes::install_github("snikumbh/archR", INSTALL_opts = c("--no-test-load"))

Contact

Comments, suggestions, enquiries/requests are welcome! Feel free to email or create an new issue