| cbDistMatrix |
cbDistMatrix function: Calculates pairwise distance matrix from DNA k-mer counts based on a modified Canberra distance. |
| cbDistMatrix-method |
cbDistMatrix function: Calculates pairwise distance matrix from DNA k-mer counts based on a modified Canberra distance. |
| cbDistMatrix-methods |
cbDistMatrix function: Calculates pairwise distance matrix from DNA k-mer counts based on a modified Canberra distance. |
| char2ascii |
ascii2char: Converting ASCII encoded values to character values. |
| collectDur |
collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files. |
| collectDur-method |
collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files. |
| collectDur-methods |
collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files. |
| collectTime |
collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files. |
| collectTime-method |
collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files. |
| collectTime-methods |
collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files. |
| countDnaKmers |
countDnaKmers: Counting k-mers in DNA sequence. |
| countFastaKmers |
countFastaKmers function: Counts DNA k-mers from (compressed) fasta files. |
| countGenomeKmers |
countGenomeKmers: Counting K-mers in DNA sequences. |
| countSpliceKmers |
countSpliceKmers: Counting K-mers on donor (5', upstream) sides (exonic) of splice sites. |
| maxSeqLen |
Class '"Fastqq"' |
| maxSeqLen-method |
Class '"Fastqq"' |
| maxSeqLen-methods |
Class '"Fastqq"' |
| meltDownK |
meltDownK: Condensing DNA k-mer count data to lower k-value (i.e. shorter DNA motifs). |
| meltDownK-method |
meltDownK: Condensing DNA k-mer count data to lower k-value (i.e. shorter DNA motifs). |
| meltDownK-methods |
meltDownK: Condensing DNA k-mer count data to lower k-value (i.e. shorter DNA motifs). |
| mergedPhred |
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects. |
| mergedPhred-method |
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects. |
| mergedPhred-methods |
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects. |
| mergedPhredQuantiles |
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects. |
| mergedPhredQuantiles-method |
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects. |
| mergedPhredQuantiles-methods |
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects. |
| mergeFastqq |
mergeFastqq: Merges two Fastqq object into one. |
| mergeFastqq-method |
mergeFastqq: Merges two Fastqq object into one. |
| mergeFastqq-methods |
mergeFastqq: Merges two Fastqq object into one. |
| phred |
Class '"Fastqq"' |
| phred-method |
Class '"Fastqq"' |
| phred-methods |
Class '"Fastqq"' |
| phredDist |
phredDist: Global relative content of Phred values in Fastqq objects (or subsets). |
| phredDist-method |
phredDist: Global relative content of Phred values in Fastqq objects (or subsets). |
| phredDist-methods |
phredDist: Global relative content of Phred values in Fastqq objects (or subsets). |
| phredQuantiles |
Class '"Fastqq"' |
| phredQuantiles-method |
Class '"Fastqq"' |
| phredQuantiles-methods |
Class '"Fastqq"' |
| phredTable |
phredTable: Returns a data.frame with phred encodings. |
| plotGCcontent |
plotGCcontent: Plots the proportions of relative GC content for all FASTQ files. |
| plotGCcontent-method |
plotGCcontent: Plots the proportions of relative GC content for all FASTQ files. |
| plotGCcontent-methods |
plotGCcontent: Plots the proportions of relative GC content for all FASTQ files. |
| plotKmerCount |
plotKmerCount: Creation of plots DNA for k-mer counts from Fastqq objects. |
| plotKmerCount-method |
plotKmerCount: Creation of plots DNA for k-mer counts from Fastqq objects. |
| plotKmerCount-methods |
plotKmerCount: Creation of plots DNA for k-mer counts from Fastqq objects. |
| plotMergedPhredQuant |
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects. |
| plotMergedPhredQuant-method |
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects. |
| plotMergedPhredQuant-methods |
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects. |
| plotNucCount |
plotNucCount: Plots nucleotide counts from Fastqq objects. |
| plotNucCount-method |
plotNucCount: Plots nucleotide counts from Fastqq objects. |
| plotNucCount-methods |
plotNucCount: Plots nucleotide counts from Fastqq objects. |
| plotNucFreq |
plotNucFreq: Plots the position wise relative nucleotide content for nucleotides 'A','C','G','T'. |
| plotNucFreq-method |
plotNucFreq: Plots the position wise relative nucleotide content for nucleotides 'A','C','G','T'. |
| plotNucFreq-methods |
plotNucFreq: Plots the position wise relative nucleotide content for nucleotides 'A','C','G','T'. |
| plotPhredDist |
phredDist: Global relative content of Phred values in Fastqq objects (or subsets). |
| plotPhredDist-method |
phredDist: Global relative content of Phred values in Fastqq objects (or subsets). |
| plotPhredDist-methods |
phredDist: Global relative content of Phred values in Fastqq objects (or subsets). |
| plotPhredQuant |
plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and 90 % quantiles of phred values. |
| plotPhredQuant-method |
plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and 90 % quantiles of phred values. |
| plotPhredQuant-methods |
plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and 90 % quantiles of phred values. |
| probeLabel |
Class '"Fastqq"' |
| probeLabel-method |
Class '"Fastqq"' |
| probeLabel-methods |
Class '"Fastqq"' |
| probeLabel<- |
Class '"Fastqq"' |
| probeLabel<--method |
Class '"Fastqq"' |
| probeLabel<--methods |
Class '"Fastqq"' |
| propPhred |
propPhred: Lane specific proportion of reads in a specified Phred-region. |
| propPhred-method |
propPhred: Lane specific proportion of reads in a specified Phred-region. |
| propPhred-methods |
propPhred: Lane specific proportion of reads in a specified Phred-region. |