/usr/lib/R/site-library/Biostrings/doc/BiostringsQuickOverview.Rnw is in r-bioc-biostrings 2.42.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 | %\VignetteIndexEntry{Biostrings Quick Overview}
%\VignetteKeywords{DNA, RNA, Sequence, Biostrings, Sequence alignment}
%\VignettePackage{Biostrings}
%
% NOTE -- ONLY EDIT THE .Rnw FILE!!! The .tex file is
% likely to be overwritten.
%
\documentclass[10pt]{article}
\usepackage{times}
\usepackage{hyperref}
\usepackage[margin=0.65in]{geometry}
\newcommand{\scscst}{\scriptscriptstyle}
\newcommand{\scst}{\scriptstyle}
\newcommand{\R}{{\textsf{R}}}
\newcommand{\code}[1]{{\texttt{#1}}}
\newcommand{\term}[1]{{\emph{#1}}}
\newcommand{\Rpackage}[1]{\textsf{#1}}
\newcommand{\Rfunction}[1]{\texttt{#1}}
\newcommand{\Robject}[1]{\texttt{#1}}
\newcommand{\Rclass}[1]{{\textit{#1}}}
\newcommand{\Rmethod}[1]{{\textit{#1}}}
\newcommand{\Rfunarg}[1]{{\textit{#1}}}
\bibliographystyle{plainnat}
\begin{document}
%\setkeys{Gin}{width=0.55\textwidth}
\title{Biostrings Quick Overview}
\author{Herv\'e Pag\`es \\
Fred Hutchinson Cancer Research Center \\
Seattle, WA}
\date{\today}
\maketitle
%\tableofcontents
Please note that \emph{most} but \emph{not all} the functionalities
provided by the \Rpackage{Biostrings} package are listed in this
document.
%-----------------------------------------------------------------------------
\begin{table}[ht]
\begin{center}
\begin{tabular}{p{2.5in}|p{4in}}
{\bf Function} & {\bf Description} \\
\hline
\Rfunction{length} & Return the number of sequences in an object. \\
\hline
\Rfunction{names} & Return the names of the sequences in an object. \\
\hline
\Rfunction{[} & Extract sequences from an object. \\
\hline
\Rfunction{head}, \Rfunction{tail} & Extract the first or last sequences
from an object. \\
\hline
\Rfunction{rev} & Reverse the order of the sequences in an object. \\
\hline
\Rfunction{c} & Combine in a single object the sequences from 2 or more objects. \\
\hline
\Rfunction{width}, \Rfunction{nchar} & Return the sizes (i.e. number of
letters) of all the sequences in an object.\\
\hline
\Rfunction{==}, \Rfunction{!=} & Element-wise comparison of the sequences
in 2 objects. \\
\hline
\Rfunction{match}, \Rfunction{\%in\%} &
Analog to \Rfunction{match} and \Rfunction{\%in\%} on character vectors. \\
\hline
\Rfunction{duplicated}, \Rfunction{unique} &
Analog to \Rfunction{duplicated} and \Rfunction{unique} on character
vectors. \\
\hline
\Rfunction{sort}, \Rfunction{order} &
Analog to \Rfunction{sort} and \Rfunction{order} on character vectors,
except that the ordering of DNA or Amino Acid sequences doesn't
depend on the locale. \\
\hline
\Rfunction{relist}, \Rfunction{split}, \Rfunction{extractList} &
Analog to \Rfunction{relist} and \Rfunction{split} on character vectors,
except that the result is a \Rclass{DNAStringSetList} or
\Rclass{AAStringSetList} object.
\Rfunction{extractList} is a generalization of \Rfunction{relist} and
\Rfunction{split} that supports \emph{arbitrary} groupings. \\
\hline
\end{tabular}
\end{center}
\caption{\bf Low-level manipulation of \Rclass{DNAStringSet} and
\Rclass{AAStringSet} objects.}
\label{table:Low_level_manipulation}
\end{table}
%-----------------------------------------------------------------------------
\begin{table}[ht]
\begin{center}
\begin{tabular}{p{2.5in}|p{4in}}
{\bf Function} & {\bf Description} \\
\hline
\Rfunction{alphabetFrequency}\par
\Rfunction{letterFrequency} &
Tabulate the letters (all the letters in the alphabet for
\Rfunction{alphabetFrequency}, only the specified letters for
\Rfunction{letterFrequency}) of a sequence or set of sequences. \\
\hline
\Rfunction{letterFrequencyInSlidingView} &
Specialized version of \Rfunction{letterFrequency} that tallies the
requested letter frequencies for a fixed-width view that is conceptually
slid along the input sequence. \\
\hline
\Rfunction{consensusMatrix} &
Computes the consensus matrix of a set of sequences. \\
\hline
\Rfunction{dinucleotideFrequency}\par
\Rfunction{trinucleotideFrequency}\par
\Rfunction{oligonucleotideFrequency} &
Fast 2-mer, 3-mer, and k-mer counting for DNA or RNA. \\
\hline
\Rfunction{nucleotideFrequencyAt} &
Tallies the short sequences formed by extracting the nucleotides found
at a set of fixed positions from each sequence of a set of DNA or RNA
sequences. \\
\hline
\end{tabular}
\end{center}
\caption{\bf Counting / tabulating.}
\label{table:Counting_tabulating}
\end{table}
%-----------------------------------------------------------------------------
\begin{table}[ht]
\begin{center}
\begin{tabular}{p{2.5in}|p{4in}}
{\bf Function} & {\bf Description} \\
\hline
\Rfunction{reverse}\par
\Rfunction{complement}\par
\Rfunction{reverseComplement} &
Compute the reverse, complement, or reverse-complement, of a set of
DNA sequences. \\
\hline
\Rfunction{translate} &
Translate a set of DNA sequences into a set of Amino Acid sequences. \\
\hline
\Rfunction{chartr} & Translate the letters in a set of sequences. \\
\hline
\Rfunction{subseq}, \Rfunction{subseq<-}\par
\Rfunction{extractAt}, \Rfunction{replaceAt} &
Extract/replace arbitrary substrings from/in a string or set of strings. \\
\hline
\Rfunction{replaceLetterAt} & Replace the letters specified by a set of
positions by new letters. \\
\hline
\Rfunction{padAndClip}, \Rfunction{stackStrings} & Pad and clip strings. \\
\hline
\Rfunction{unstrsplit} & A fast implementation of
\code{sapply(x, paste0, collapse=sep)} for collapsing the list elements
of a \Rclass{DNAStringSetList} or \Rclass{AAStringSetList} object. \\
\hline
\end{tabular}
\end{center}
\caption{\bf Sequence transformation and editing.}
\label{table:Sequence_editing}
\end{table}
%-----------------------------------------------------------------------------
\begin{table}[ht]
\begin{center}
\begin{tabular}{p{2.5in}|p{4in}}
{\bf Function} & {\bf Description} \\
\hline
\Rfunction{matchPattern}\par
\Rfunction{countPattern} &
Find/count all the occurrences of a given pattern (typically short)
in a reference sequence (typically long).
Support mismatches and indels. \\
\hline
\Rfunction{vmatchPattern}\par
\Rfunction{vcountPattern} &
Find/count all the occurrences of a given pattern (typically short)
in a set of reference sequences.
Support mismatches and indels. \\
\hline
\Rfunction{matchPDict}\par
\Rfunction{countPDict}\par
\Rfunction{whichPDict} &
Find/count all the occurrences of a set of patterns in a reference
sequence. (\Rfunction{whichPDict} only identifies which patterns in
the set have at least one match.)
Support a small number of mismatches. \\
\hline
\Rfunction{vmatchPDict}\par
\Rfunction{vcountPDict}\par
\Rfunction{vwhichPDict} &
[Note: \Rfunction{vmatchPDict} not implemented yet.]
Find/count all the occurrences of a set of patterns in a set of
reference sequences. (\Rfunction{whichPDict} only identifies for each
reference sequence which patterns in the set have at least one match.)
Support a small number of mismatches. \\
\hline
\Rfunction{pairwiseAlignment} &
Solve (Needleman-Wunsch) global alignment, (Smith-Waterman) local
alignment, and (ends-free) overlap alignment problems. \\
\hline
\Rfunction{matchPWM}\par
\Rfunction{countPWM} &
Find/count all the occurrences of a Position Weight Matrix in a reference
sequence. \\
\hline
\Rfunction{trimLRPatterns} &
Trim left and/or right flanking patterns from sequences. \\
\hline
\Rfunction{matchLRPatterns} &
Find all paired matches in a reference sequence i.e. matches specified by
a left and a right pattern, and a maximum distance between them. \\
\hline
\Rfunction{matchProbePair} &
Find all the amplicons that match a pair of probes in a reference
sequence. \\
\hline
\Rfunction{findPalindromes} &
Find palindromic regions in a sequence. \\
\hline
\end{tabular}
\end{center}
\caption{\bf String matching / alignments.}
\label{table:String_matching_alignments}
\end{table}
%-----------------------------------------------------------------------------
\begin{table}[ht]
\begin{center}
\begin{tabular}{p{2.5in}|p{4in}}
{\bf Function} & {\bf Description} \\
\hline
\Rfunction{readBStringSet}\par
\Rfunction{readDNAStringSet}\par
\Rfunction{readRNAStringSet}\par
\Rfunction{readAAStringSet} &
Read ordinary/DNA/RNA/Amino Acid sequences from files (FASTA or FASTQ
format). \\
\hline
\Rfunction{writeXStringSet} &
Write sequences to a file (FASTA or FASTQ format). \\
\hline
\Rfunction{writePairwiseAlignments} &
Write pairwise alignments (as produced by \Rfunction{pairwiseAlignment})
to a file (``pair'' format). \\
\hline
\Rfunction{readDNAMultipleAlignment}\par
\Rfunction{readRNAMultipleAlignment}\par
\Rfunction{readAAMultipleAlignment}&
Read multiple alignments from a file (FASTA, ``stockholm'',
or ``clustal'' format). \\
\hline
\Rfunction{write.phylip} &
Write multiple alignments to a file (Phylip format). \\
\hline
\end{tabular}
\end{center}
\caption{\bf I/O functions.}
\label{table:I_O_functions}
\end{table}
%-----------------------------------------------------------------------------
\begin{table}[ht]
\begin{center}
\begin{tabular}{p{2.5in}|p{4in}}
{\bf Function} & {\bf Description} \\
\hline
\Rfunction{stringDist} &
Computes the matrix of Levenshtein edit distances, or Hamming distances,
or pairwise alignment scores, for a set of strings. \\
\hline
\end{tabular}
\end{center}
\caption{\bf Miscellaneous.}
\label{table:Miscellaneous}
\end{table}
\end{document}
|