extract.lib {sagenhaft} | R Documentation

## Functions for SAGE library extraction

### Description

Functions to extract the tags in a library from sequences or base-caller output.

### Usage

    extract.lib.from.zip(zipfile, libname=sub(".zip","",basename(zipfile)),
                         ...)
    extract.lib.from.directory(dirname, libname=basename(dirname),
                               pattern="(\.phd\.1\$)|(\.seq\$)", ...)
    extract.library.tags(filelist, base.caller.format="phd",
                         remove.duplicate.ditags=TRUE,
                         remove.N=FALSE, remove.low.quality=10,
                         taglength=10, min.ditag.length=(2*taglength-2),
                         max.ditag.length=(2*taglength+4),
                         cut.site="catg", default.quality=NA, verbose=TRUE,
                         ...)
    reestimate.lib.from.tagcounts(tagcounts, libname, default.quality=20, ...)
    compute.unique.tags(lib)
    combine.libs(..., artifacts=c("Linker", "Ribosomal", "Mitochondrial"))
    remove.sage.artifacts(lib,
                          artifacts=c("Linker","Ribosomal","Mitochondrial"),
                          ...)
    read.phd.file(file)
    read.seq.qual.filepair(file, default.quality=NA)
    extract.ditags(sequence, taglength=10, filename=NA,
                   min.ditag.length=(2*taglength-2),
                   max.ditag.length=(2*taglength+4), cut.site="catg")

### Arguments

`zipfile,dirname` | Name of a ZIP file or a directory that contains base-caller output files
`libname` | `libname` a character string to be assigned as library name
`pattern` | Regular expression to specify pattern for the files that will be read
`filelist` | List of files to be read
`base.caller.format` | `base.caller.format` can be "phd" or "seq" or a character vector of the length of the filelist
`remove.duplicate.ditags` | Remove duplicate ditags. TRUE or FALSE
`remove.N` | Remove all tags that contain N. TRUE or FALSE
`remove.low.quality` | Remove all tags with an average quality score of less than `remove.low.quality`. Skipped if < 0
`taglength` | Length of tags. Usually 10 or 17
`min.ditag.length,max.ditag.length` | Minimum and maximum length for ditags
`cut.site` | Restriction enzyme cut site. Usually CATG
`verbose` | Display information during process
`lib` | Library object
`file,filename` | Character string indicating file name
`default.quality` | Quality value to use on sequences, if quality files are missing
`sequence` | Construct containing sequence and quality values returned by read.phd.file or read.seq.qual.filepair
`artifacts` | Types of artificially generated tags to remove.
`...` | Arguments passed on to extraction functions.
`tagcounts` | Tagcounts from library. Integer Vecotor with Tag sequences as names.

### Details

The functions `extract.lib.from.zip` or `extract.lib.from.directory` should be used to extract the SAGE TAGS from the sequences of a library, the sequences need to be provided by the output files from the base caller software either in a ZIP archive or in a directory. These are usually the only functions that should directly be called by the user. The other functions are called by these and should only be used directly by experienced users to get more direct control over the process. Most arguments are passed on and can be specified in the high level functions. Zipfilenames must be specified using relative pathnames!

### Value

`lib` returns an SAGE library object.

### Author(s)

Tim Beissbarth

### References

http://tagcalling.mbgproject.org

### See Also

`sage.library`, `error.correction`

### Examples

    library(sagenhaft)
    file.copy(system.file("data/E15postHFI.zip",package="sagenhaft"),
              "E15postHFI.zip")
    E15post<-extract.lib.from.zip("E15postHFI.zip", taglength=10,
                                  min.ditag.length=20, max.ditag.length=24)
    E15post

[Package sagenhaft version 1.2.0 Index]