Package index • MetaScope

MetaDemultiplex (optional)

Obtain non-barcoded sequencing reads.

meta_demultiplex(): Demultiplexing sequencing reads

MetaRef

Obtain target and filter genome sequences from NCBI nucleotide database and index using the Bowtie 2 or Subread aligner

download_refseq(): Download RefSeq genome libraries

mk_bowtie_index(): Make a Bowtie2 index

mk_subread_index(): Make a Subread index

download_accessions(): Download indexes required for MetaScope ID and MetaBlast modules

MetaAlign

Align sequencing reads to indexed target genome sequences

align_target(): Align microbiome reads to a set of reference libraries

align_target_bowtie(): Align microbiome reads to set of indexed Bowtie2 libraries

align_details: A universal parameter settings object for Rsubread alignment

bt2_16S_params: A universal parameter object for Bowtie 2 16S alignment

bt2_regular_params: A universal parameter object for Bowtie 2 metagenomic or non-16S alignment

bt2_missing_params: A universal parameter object for Bowtie 2 metagenomic alignment where the host genome is thought to be absent from the reference database

MetaFilter

Remove reads mapped to indexed host genome sequences

filter_host(): Use Rsubread to align reads against one or more filter libraries and subsequently remove mapped reads

filter_host_bowtie(): Use Rbowtie2 to align reads against one or more filter libraries and subsequently remove mapped reads

MetaID

Reassign ambiguously mapped reads to probable source genome

metascope_id(): Identify which genomes are represented in a processed sample

MetaCombine

Aggregate samples into a MultiAssayExperiment compatible with the animalcules package

convert_animalcules(): Create a multi-assay experiment from MetaScope output for usage with animalcules

convert_animalcules_silva(): Create a multi-assay experiment from MetaScope output for usage with animalcules with the SILVA 13_8 database

convert_animalcules_patho(): Create a multi-assay experiment from PathoScope 2.0 output for usage with animalcules

Helper Functions

These functions were developed to aid in carrying out other primary functions.

remove_matches(): Helper function to remove reads matched to filter libraries

combined_header(): Create a combined .bam header

bam_reheader_R(): Replace the header from a .bam file

get_children(): Get child nodes from NCBI taxonomy

merge_bam_files(): Merge multiple .bam files

count_matches(): Count the number of base lengths in a CIGAR string for a given operation

extract_reads(): Helper function for demultiplexing

locations(): Helper Function for MetaScope ID

filter_unmapped_reads(): Filter unmapped reads

check_samtools_exists(): Check if samtools exists on the system