embed_asv_table_new: EmbedAsvTable

In MaudeDavidLab/GMEmbeddings: Creates a Matrix of Embeddings

EmbedAsvTable

Usage

EmbedAsvTable(seqtab, fasta_file, blast_hits, embedding_matrix)

Arguments

seqtab	The seqtab argument needs to be an object. If not already an object, use the getSeqtab function to change the seqtab file into something that the EmbedAsvTable function can use as an argument.
fasta_file	The fasta_file argument needs to be a string. This string will contain the full file name of your fasta file.
blast_hits	The blast_hits argument needs to be passed in as an object. If not an object, the EmbedAsvTable function will not work properly.
embedding_matrix	The embedding_matrix argument needs to be passed in as a string. This string should contain the full file name of your embedding matrix.

Examples

## The function is currently defined as
EmbedAsvTable <- function(seqtab, fasta_file_name, blast_hits, embedding_file_name){

  best_hits = getBestHits(blast_hits = blast_hits, id_thresh = 99)

  seqtab <- embedSeqtab(seqtab, fasta_file = fasta_file_name, best_hits = best_hits, embedding_file_name)

  seqtab
}

MaudeDavidLab/GMEmbeddings documentation built on March 31, 2022, 3:12 a.m.