query sequence, a character string (probably representing
a transcript of interest), is scanned for the presence of exact
matches to the sequences in the character vector
The indices of the set of matches are returned.
The function is inefficient: it works on R's character vectors, and
the actual matching algorithm is of time complexity
matchPDict for more efficient sequence matching functions.
A character vector. For example, each element may represent a gene (transcript) of interest. See Details.
A character vector. For example, each element may represent the probes on a DNA array.
A logical value. If TRUE, return also the start positions of the matches in the query sequence.
toupper is applied to the arguments
records before matching. The intention of this is to make
the matching case-insensitive.
The function is embarrassingly naive.
The matching is done using the C library function
A list. Its first element is a list of the same length as the input vector. Each element of the list is a numeric vector containing the indices of the probes that have a perfect match in the query sequence.
probepos is TRUE,
the returned list has a second element: it is of the same shape
as described above, and gives the respective positions of the
R. Gentleman, Laurent Gautier, Wolfgang Huber
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Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: IRanges Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: hgu95av2probe Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'hgu95av2probe'
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