An R package to enable organisation and visualisation of nanopore sequencing data

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Documentation for package ‘poRe’ version 0.24

Help Pages

are.my.data.basecalled Checks whether a directory of fast5 files have been basecalled
copy.runs Process the MinION run folder and copy fast5 files to appropriate sub folders
coreImagePlot Code from http://www.phaget4.org/R/image_matrix.html. Plot a matrix as a heatmap.
extract.run.fasta Extract fasta data from a directory of fast5 files
extract.run.fastq Extract fastq data from a directory of fast5 files
extractfasta Extract fasta data from a single fast5 file
extractfastq Extract fastq data from a single fast5 file
fast52fasta Extract fasta data from a single fast5 file and write to a file
fast52fastq Extract fastq data from a single fast5 file and write to a file
get.align Get the saignment table from a fast5 file
get.events Extract events from a single fast5 file
get.kmer.events Join the alignment table and the two events tables
get.model.params Extract model parameters from a fast5 file
get.models Extract models from a single fast5 file
get_analysis_name Internal function
get_barcode Internal function
get_channel_number Internal function
get_essential_info Extract meta data from a single fast5 file
get_experiment_start_time Internal function
get_fast5_info Extract meta data from a single fast5 file
get_fasta Extract fasta data from a single fast5 file as a list
get_fastq Extract fastq data from a single fast5 file as a list
get_meta_info Extract meta data from a single fast5 file
get_read_number_and_id Internal function
get_run_id Internal function
get_sampling_rate Internal function
get_sequence_lengths Internal function
get_start_time Internal function
get_summary_stuff Internal function
get_time_stamp Internal function
get_tracking_attributes Internal function
map.2dfastq.events Map position of kmer in the 2D fastq sequence to template and complement events that created it
MINION Metadata from a very early MinION run at Edinburgh Genomics. From 'read.fast5.info'
MINIONEVENTS EVents data from a MinION fast5 file
plot.as.squiggle Plot a theoretical "squiggle" of a vector of numbers representing model means
plot.channel.reads Barplot of the number of reads per channel
plot.channel.summary Creates heatmap of the MinION flowcell layout
plot.channel.yield Barplot of the yield per channel
plot.cumulative.yield Plot cumulative yield for a MinION run
plot.length.histogram Plot length histogram for a MinION run
plot.squiggle Plot a theoretical "squiggle" of events from a MinION nanopore read
pore_parallel Experimental GUI for MinION data extraction
pore_rt Experimental GUI for MinION run monitoring
printfasta Print fasta data from a single fast5 file to STDOUT
printfastq Print fastq data from a single fast5 file to STDOUT
read.essential.info Extract meta data from a directory of fast5 files
read.fast5.info Extract meta data from a directory of fast5 files
read.meta.info Extract meta data from a directory of fast5 files
run.summary.stats Extracts key run stats for a MinION run
show.layout Show the MinION flowcell layout by channel number
summarise.by.channel Calculate a load of statistics for a MinION run summarised by channel. Takes the output of 'read.meta.info'