read.resultsGFF

fnames

path

A data.frame containing sample information, one row per
    sample, in the same order as the files in fnames

samples

A character vector for notes--not currently stored

notes

Number of lines to skip if the file contains a header

skip

The field separator--should be a tab character for gff
    files, but can be set if necessary.

The text quote character--again not used for gff file, typically

quote


  A GFF format file is a quite flexible format for storing genomic
  data.  Nimblegen uses these format files as one format for making
  chip-chip data available.  This function reads these files, one per
  experiment and creates a resulting aGFF-class object.


manip

ACME (Algorithms for Calculating Microarray Enrichment) is
a set of tools for analysing tiling array ChIP/chip, DNAse
hypersensitivity, or other experiments that result in regions
of the genome showing "enrichment".  It does not rely on a
specific array technology (although the array should be a
"tiling" array), is very general (can be applied in experiments
resulting in regions of enrichment), and is very insensitive to
array noise or normalization methods.  It is also very fast and
can be applied on whole-genome tiling array experiments quite
easily with enough memory.

Sean Davis

ACME

Algorithms for Calculating Microarray Enrichment (ACME)

read.resultsGFF function

A GFF format file is a quite flexible format for storing genomic
  data.  Nimblegen uses these format files as one format for making
  chip-chip data available.  This function reads these files, one per
  experiment and creates a resulting aGFF-class object.

read.resultsGFF: Read Nimblegen GFF files

Description

Usage

Arguments

Value

Details

References

See Also

Examples