Man pages for sherrillmix/dnar
Miscellaneous functions to deal with bioinformatic analyses

aa2codonsFind the DNA to code for a given amino acid
aa2dnaConvert amino acids to dna regex
adjustWindowConvenience function for selecting multiple elements from a...
allSameLengthConvenience function to check all args are same length
ambiguous2regexConverts ambiguous dna to an appropriate regular expression
ambiguousBaseCodesAmbiguous base codes
aminoAcidsAmino acid for RNA codons
anyArgsNAConvenience function to check whether any args have NAs
arrowFind coords for plotting horizontal arrows
bases2ambiguousConvert set of single bases to ambiguous code
binary2rangeFind covered ranges in binary data
blat2exonsTake coordinates of blat matches and split into a single line...
blatFindGapsFind gaps in blat coordinates
blatReadsVsRefsMake a 2bit file from one set of reads and blat another set...
blockToAlignConvert blocks from blat into alignment
cacheOperationCache an operation to disk or load if cache file present
chaoCalculate chao diversity index
checkBlatCheck if blat is running on port
chooseAtLeastOneFromEachCalculate the number of combinations possible from nGroups...
cigarToBlockConvert cigar and starts to qStarts, tStarts, blockSizes as...
cleanMclapplyA function to break an mclapply into parts, save to disk and...
codons2aaConvert codon to amino acid
complementDnaComplement DNA
conservativeBoundaryGet the conservative edge of a confidence interval
convertLineToUserConvert from axis line to user coordinates
convertUserToLineConvert from user coordinates to axis line
countNmersCount nMers in a string
cumpasteCumulative paste convenience function
cutBlatReadsTake the output from blat and make continous reads out of it
cv.glm.parCheck predictions of glm by cross validation
degapRemove gap characters from DNA sequences
dna2aaConvert dna/rna to amino acids
dna2codonsConvert DNA string into seperate codons
escapeRegexBracketCharsConvenience function to escape characters for insertion into...
expandAmbiguousConvert ambiguous dna to all possible sequences
fillCoverFill zeros in cover data
fillDownConvenience function to fill values down a column
fillListLoop through list, get unique names and make sure every...
fillZerosFill missing position with zeros
findIntronsConvert set of starts and ends of exons to introns
flow2seqConvert 454 flows to DNA sequences
gap2NoGapConvert gapped coordinates to what the coordinates would be...
gcPercentCalculate GC percentage for strings
generateFastaGenerate fake name and sequence data
giniCalculate Gini index
highlightDifferencesSwitch the case of positions in seq1 that mismatch seq2
highlightStringFind pattern in strings and flip case
index2rangeFind covered ranges with numerical index data
indexFlowFind flow corresponding to a given base position
indexMatrixConvenience function for selecting multiple elements from a...
insetScaleAdd an inset color scale to a plot
intsToQualConvert fastq chars to integer quals
isErrorConvenience function to check for errors in a list of results...
jensenShannonCalculate Jensen Shannon divergence between two probability...
killBlatKill blat running on a given port
kullbackCalculate Kullback-Leibler divergence between two probability...
lagNAConvenience function for lagging with NA
liftCoordsRun liftover to convert coordinates from one genome version...
logAxisAdd a pretty log axis to a plot
mostAbundantConvenience function for picking first most abundant of a set...
movingStatCalculating a moving average/max/min statistic over a vector
multiBlatReadsVsRefsRun blatReadsVsRefs in parallel
multiRunBlatNoServerRun blat from parallel blat executables
noGap2GapConvert ungapped coordinates to what the coordinates would be...
object.sizesConvenience function to list objects by size
orderInFind the order of one vector in another
parseRegionParse a region string into chr, start, end and strand
pasteRegionMake region from chr start end
pRareCalculate the probability of observing observedX species from...
pullRegionPull counts from a bam file for target region
pwmGenerate a PWM for a set of sequences
pwmToSeqCalculate sequence for PWM
qualToIntsConvert fastq chars to integer quals
rainbow.labRainbow based on circle of lab color space
raoCalculate Rao diversity of a vector
rareEquationCalculate rarefaction using formula
rarefyCalculate rarefaction using boostrapping
rarefyCountsGenerate rarefied counts from a vector of counts
read.aceRead an ace file
read.bedRead a bed file
read.blastRead a tab-delimited blast file
read.blatRead a blat file
read.faRead a fasta file
readFaDirRead in a bunch of fasta files in a target directory
read.fastqRead fastq file
readLargeBlatRead a large blat file piece by piece
read.phdRead a single-read Sanger phred .phd file
read.samRead a sam file
read.wiggleRead a UCSC wiggle file
revCompReverse complement dna
reverseAmbiguousReverse lookup for ambiguous base codes
reverseStringReverse strings
runBlatStart a blat server, run blat on file and kill blat server
runBlatNoServerRun blat from blat executable instead of gfserver/client
samFlagTest sam flags for values
samFlagsSAM/BAM flags
samViewCall samtools view on a sam/bam file
scoreFromPWMCalculate PWM scores for sequences
seq2flowConvert a DNA sequence into expected 454 flows
seqSplitConvenience function for splitting a bunch of sequences into...
shannonCalculate Shannon diversity of a vector
slantAxisLabel axis with slanted labels
stackRegionsStack regions into smallest number of lines (using greedy...
startBlatStart a blat server
stopErrorGenerate an error
table2vectorConvenience function for converting 1-d table to named vector
toggleCaseSwap case of a string
trimNsTrim ambiguous sequence from ends of reads
unifracMatrixCalculate the shared branch length from a matrix of taxonomic...
wilsonIntCalculate the Wilson score interval
withAsAlternative with() function with explicit naming
write.faWrites sequences to a fasta file
write.fastqWrites a fastq file
sherrillmix/dnar documentation built on Sept. 12, 2017, 9:30 p.m.