Simple class representing a file of Fasta format sequences and each ones\nlength\n"],["Bio::DB::Pileup","","Bio/DB/Pileup.html","","
Extends the methods of the Bio::DB::Pileup class in bio-samtools. A pileup\nobject represents the SAMtools …\n"],["Bio::DB::Vcf","","Bio/DB/Vcf.html","","
Extends the methods of the Bio::DB::Vcf class in bio-samtools. A Vcf object\nrepresents the VCF format …\n"],["Bio::Util","","Bio/Util.html","",""],["Bio::Util::Gngm","","Bio/Util/Gngm.html","","
A Bio::Util::Gngm object represents a single region on a reference genome\nthat is to be examined using …\n"],["alternatives","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-alternatives","()","
List of alternate alleles at this locus, obtained by splitting the vcf.alt\nattribute string on commas …\n"],["calculate_clusters","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-calculate_clusters","( opts={} )","
Calculates the k-means clusters of density curves (groups threads into\nbands), [density curve y values] …\n"],["calculate_densities","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-calculate_densities","(adjust=1)","
Sets and returns the array of arrays [window, [density curve x\nvalues], [density curve y values] ] Calculates …\n"],["calculate_signal","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-calculate_signal","()","
Returns an array of values representing the ratio of average of the\nexpected threads/windows to the control …\n"],["close","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-close","()","
for BAM files calls Bio::DB::Sam#close to close the connections to input\nfiles safely\n"],["clusters","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-clusters","(opts={})","
Returns the array instance variable @clusters. The R function +kmeans()+ is\nused to calculate the clusters …\n"],["collect_threads","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-collect_threads","(options={})","
Resets contents of instance variable @threads and returns an array of\narrays [[window 1, snp position …\n"],["densities","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-densities","(adjust=1)","
Returns the instance variable @densities array of arrays [window,\n[density curve x values], [density …\n"],["discordant_chastity","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-discordant_chastity","()","
calculates the discordant chastity statistic as defined in Austin et al\n(2011) bar.utoronto.ca/ngm/description.html …\n"],["draw_bands","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-draw_bands","(file=\"myfile.png\", optsa={})","
Draws the clustered bands that correspond to the expected and control\nwindow in a single PNG file file …\n"],["draw_hit_count","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-draw_hit_count","(file=\"myfile.png\",opts=@opts[:graphics])","
Draws a barplot of the number of polymorphisms in each thread/window in a\nsingle PNG file file\n"],["draw_peaks","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-draw_peaks","(file=\"myfile.png\",opts=@opts[:graphics])","
Draws the peaks calculated from the signal curve by the R function\nPeaks in Bio::Util::Gngm#calculate_peaks …\n"],["draw_signal","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-draw_signal","(file=\"myfile.png\", opts=@opts[:graphics])","
Draws the contents of the @signal instance variable in a single PNG file\nfile\n"],["draw_threads","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-draw_threads","(file=\"myfile.png\", options={})","
Draws the threads in a single PNG file file\n
Options and defaults\n
:draw_legend => nil -if a filename …\n"],["each","Bio::DB::FastaLengthDB","Bio/DB/FastaLengthDB.html#method-i-each","()",""],["frequency_histogram","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-frequency_histogram","(file=\"myfile.png\", bin_width=@opts[:histo_bin_width], opts=@opts[:graphics])","
Draws a histogram of polymorphism frequencies across the reference genome\nsection defined in Bio::Util::Gngm#initialize …\n"],["get_band","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-get_band","(window=1.0)","
gets an array of windows that cluster with a given window\n"],["get_insert_size_frequency","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-get_insert_size_frequency","(options={})","
Returns array of arrays [[window start position, proportion of\nalignments > insert size]]. Does this …\n"],["get_peaks","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-get_peaks","(opts=@opts[:peaks])","
private Calculates the position of peaks in the signal curve\n"],["get_unmapped_mate_frequency","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-get_unmapped_mate_frequency","(options={})","
Returns array of arrays [[window start position, proportion of reads\nwith unmapped mates]]. Does this …\n"],["gq","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-gq","()","
Returns the genotype quality score from the sample data (as defined by the\nVcf GQ attribute) for the …\n"],["hit_count","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-hit_count","()","
Returns an array of polymorphisms in each thread/window <tt>[[window,\npolymorphism count] ]. Useful …\n"],["is_allowed_substitution?","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-is_allowed_substitution-3F","(ref,alt,opts)",""],["is_indel?","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-is_indel-3F","(options)","
Returns true if ref col is different in length from any of the entries in\nalt column\n"],["is_mnp?","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-is_mnp-3F","(options)","
returns true if ref col has same length as all alternatives and position\nvariant passes quality\n"],["is_snp?","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-is_snp-3F","(opts)","
returns true if self is a SNP with minimum coverage depth of\n:min_depth and minimum non-reference bases …\n"],["is_snp?","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-is_snp-3F","(options)","
returns true if ref col has length of 1 and is_mnp?\n"],["keep_known_variants","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-keep_known_variants","(file=nil)","
Deletes everything from self.snp_positions not mentioned by position in\nself.known_variants. Directly …\n"],["mq","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-mq","()","
Returns the mean Mapping Quality from the reads over this position as\ndefined by the Vcf MQ attribute. …\n"],["new","Bio::DB::FastaLengthDB","Bio/DB/FastaLengthDB.html#method-c-new","(args)",""],["new","Bio::Util::Gngm","Bio/Util/Gngm.html#method-c-new","(options)","
Returns a new Bio::Util::Gngm object.\n\n
g = Bio::Util::Gngm.new(:file => "aln.sort.bam", \n :format ...\n\n"],["non_ref_allele_count","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-non_ref_allele_count","()","
Returns the depth of reads containing the non reference allele. IE the sum\nof the last two figures in …\n"],["non_ref_allele_freq","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-non_ref_allele_freq","()","
Returns the non-reference allele frequency based on depth of reads used for\nthe genotype call,\n
IE\n\n
vcf.non_ref_allele_count ...\n"],["pass_quality?","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-pass_quality-3F","(options)","
Returns true if the position passes criteria\n
Options and Defaults:\n
:min_depth => 2\n"],["peaks","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-peaks","()","
Returns the positions of the peaks in the signal curve calculated by\nBio::Util::Gngm#get_peaks as an …\n"],["pl","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-pl","()","
Returns the phred scaled likelihood of the first non-reference allele (as\ndefined by the Vcf PL attribute) …\n"],["signal","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-signal","()",""],["snp_positions","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-snp_positions","(optsa={})","
Returns array of arrays [[position, statistic]] for\npolymorphisms passing filters in optsa Default options …\n"],["snp_positions=","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-snp_positions-3D","(arr)","
allows the user to assign SNP positions\n"],["threads","Bio::Util::Gngm","Bio/Util/Gngm.html#method-i-threads","(opts=@opts[:threads])","
Returns contents of @threads, an array of arrays [[window 1, snp\nposition 1, snp position 2 ... snp position …\n"],["to_s","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-to_s","()","
Return a short string representing chromosome, position, reference\nsequence, alt sequence(s) and the …\n"],["used_depth","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-used_depth","()","
The depth of reads actually used in the genotype call by Vcftools. The sum\nof the DP4 attribute. Returns …\n"],["variant?","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-variant-3F","()","
returns true if the alt column of the Vcf is not\n.\n
Examples\n
vcf record = 20 14370 rs6054257 G …\n"],["LICENSE","","LICENSE_txt.html","","
Copyright © 2011 Dan MacLean\n
Permission is hereby granted, free of charge, to any person obtaining a …\n"]]}}