# EaCoN : Easy Copy Number !

## Documentation for package ‘EaCoN’ version 0.3.6

- DESCRIPTION file.
- Package NEWS.

## Help Pages

Annotate | Annotation of segmented regions and generation of an HTML QC report
Annotate.ff | Annotation of segmented regions and generation of an HTML QC report, from a RDS file.
Annotate.ff.Batch | Runs Annotate.ff in batch mode with multithreading
ASCN.ASCAT | Allele-Specific Copy Number estimation using ASCAT
ASCN.FACETS | Allele-Specific Copy Number estimation using FACETS
ASCN.ff | Allele-Specific Copy Number estimation, from a RDS file.
ASCN.ff.Batch | Allele-Specific Copy Number estimation, from RDS files in batch mode, with multithreading.
ASCN.SEQUENZA | Allele-Specific Copy Number estimation using SEQUENZA
BINpack.Maker | Generates a "BINpack" containing binned data and GC tracks from a capture BED file for WES data.
CS.Process | Normalize CytoScanHD_Array arrays using Affymetrix Power Tools (APT)
CS.Process.Batch | Run CS.Process() in batch mode with multithreading
EaCoN.BedCheck | Performs checks un cleanups on a WES capture bed file
EaCoN.BedGC.chr | Compute GC-content of genomic regions defined by a BED file using chromosomic FASTA files.
EaCoN.BedGC.fasta | Compute GC-content of genomic regions defined by a BED file using a single genomic FASTA file.
EaCoN.set.bitmapType | Changes the environment variable bitmapType
GC.data | Dataset containing GC-content data
gen.df | Human gene symbols and chromosomal positions (refGene)
OS.Process | Normalize OncoScan / OncoScan_CNV arrays using Affymetrix Power Tools (APT)
OS.Process.Batch | Runs OS.Process in batch mode with multithreading
Segment.ASCAT | L2R and BAF joint segmentation using ASCAT.
Segment.FACETS | L2R and BAF joint segmentation using FACETS.
Segment.ff | L2R and BAF joint segmentation, from a RDS file.
Segment.ff.Batch | L2R and BAF joint segmentation, from a RDS file in batch mode, with multithreading.
Segment.SEQUENZA | L2R and BAF joint segmentation using SEQUENZA.
SNP6.Process | Normalize GenomeWideSNP_6 arrays using Affymetrix Power Tools (APT)
SNP6.Process.Batch | Run SNP6.Process() in batch mode with multithreading
targetlist | A restricted list of human gene symbols
WES.Bin | Computes the read depth of a pair of BAM files and bins it.
WES.Bin.Batch | Run WES.Bin() in batch mode with multithreading
WES.Normalize | Normalization of binned WES data.
WES.Normalize.ff | Normalization of binned WES data from a RDS file.
WES.Normalize.ff.Batch | Normalization of binned WES data from a RDS file in batch mode, with multithreading.