Contains quality related summarizing data on FASTQ files.
● Data Source:
BioConductor
● Keywords: classes, fastqq, kmer
● Alias: Fastqq-class
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ascii2char
(Package: seqTools) :
ascii2char: Converting ASCII encoded values to character values.
ascii2char calculates character representations for given phred values. char2ascii returns phred values for given ASCII encoded representations (the reverse transformation of ascii2char).
● Data Source:
BioConductor
● Keywords: ascii2char
● Alias: ascii2char, char2ascii
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Calculates pairwise distance matrix from DNA k-mer counts based on a modified Canberra distance. Before calculating canberra distances, read counts are normalized (in order to correct systematic effects on the distance) by scaling up read counts in each DNA k-mer count vector so that normalized read counts in each sample are nearly equal.
● Data Source:
BioConductor
● Keywords: cbDistMatrix, kmer
● Alias: cbDistMatrix, cbDistMatrix,Fastqq-method, cbDistMatrix-methods
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Objects of class Fastqq are created by reading data from FASTQ-files using the function fastqq. The fastqq function calls Sys.time() before and after execution of the core collecting routine. collectDur returns the number of seconds between these two times (as numeric value). collectTime returns the two timestamps inside a list.
● Data Source:
BioConductor
● Keywords: collectDur
● Alias: collectTime, collectTime,Fastqq-method, collectTime-methods
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countDnaKmers
(Package: seqTools) :
countDnaKmers: Counting k-mers in DNA sequence.
Counts occurrence of DNA k-mers in given DNA sequence. The k-mers are searched in a set of search windows, which are defined by start and width parameter. From each position of the search window, a DNA k-mer is identified on the right hand side on the given DNA sequence. Each value in the start vector defines the left border of a search window. The size of the search window is given by the appropriate value in the width vector. The function is intended to count DNA k-mers in selected regions (e.g. exons) on DNA sequence.
● Data Source:
BioConductor
● Keywords: countDnaKmers
● Alias: countDnaKmers
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Reads (compressed) fasta files and counts for DNA k-mers in the sequence.
● Data Source:
BioConductor
● Keywords: countFastaKmers, kmer
● Alias: countFastaKmers
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countGenomeKmers
(Package: seqTools) :
countGenomeKmers: Counting K-mers in DNA sequences.
Counts K-mers of DNA sequences inside a vector of DNA sequences. The k-mers are searched in a set of search windows, which are defined by start and width parameter. From each position of the search window, a DNA k-mer is identified on the right hand side on the given DNA sequence. Each value in the start vector defindes the left border of a search window. The size of the search window is given by the appropriate value in the width vector. The function is intended to count DNA k-mers in selected regions (e.g. exons) on DNA chromosomes while respecting strand orientation.
● Data Source:
BioConductor
● Keywords: countGenomeKmers
● Alias: countGenomeKmers
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countSpliceKmers
(Package: seqTools) :
countSpliceKmers: Counting K-mers on donor (5', upstream) sides
The function regards the given string as DNA sequence bearing a collection of splice sites. The given lEnd and rStart positions act as (1-based) coordinates of the innermost exonic nucleotides. They reside on exon-intron boundaries and have one exonic and one intronic adjacent nucleotide. The function counts width k-mers upstream on exonic DNA in reading direction (left -> right on (+) strand, right -> left on (-) strand).
● Data Source:
BioConductor
● Keywords: countSpliceKmers
● Alias: countSpliceKmers
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Reads (compressed) FASTQ files and counts for DNA k-mers for each position in sequence.
● Data Source:
BioConductor
● Keywords: fastqKmerLocs, kmer
● Alias: fastqKmerLocs
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Reads (compressed) FASTQ files and counts for given DNA k-mer subset for each position in sequence. The k-mer subset is given by a vector of k-mer indices. k-mer indices can be obtained from DNA k-mers with the function kMerIndex.
● Data Source:
BioConductor
● Keywords: fastqKmerSubsetLocs, kmer
● Alias: fastqKmerSubsetLocs
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