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

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Documentation for package ‘poRe’ version 0.24

• DESCRIPTION file.

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'