# ChIP-seq processing pipeline

## Documentation for package ‘spp’ version 1.14

- DESCRIPTION file.

## Help Pages

spp-package | ChIP-seq (Solexa) Processing Pipeline
add.broad.peak.regions | Calculate chromosome-wide profiles of smoothed tag density
find.binding.positions | Determine significant point protein binding positions (peaks)
get.binding.characteristics | Calculate characteristics of observed DNA-binding signal from cross-correlation profiles
get.broad.enrichment.clusters | Determine broad clusters of enrichment
get.conservative.fold.enrichment.profile | Estimate minimal fold enrichment/depletion along the chromosomes
get.mser | Calculate minimal saturated enrichment fold ratio
get.mser.interpolation | Interpolate MSER dependency on the tag count
get.smoothed.enrichment.mle | Calculate chromosome-wide profiles of smoothed enrichment estimate
get.smoothed.tag.density | Calculate chromosome-wide profiles of smoothed tag density
output.binding.results | Write out determined binding peaks into a text file table
read.bam.tags | Read BAM alignment file
read.bin.maqmap.tags | Read MAQ binary alignment map file
read.bowtie.tags | Read bowtie text alignment output file
read.eland.tags | Read eland output file
read.maqmap.tags | Read MAQ text alignment output file
read.meland.tags | Read modified BED tag alignment file that contains variable match length information
remove.local.tag.anomalies | Restrict or remove positions with too many tags relative to local background.
select.informative.tags | Choose informative tags
spp | ChIP-seq (Solexa) Processing Pipeline
write.broadpeak.info | Write out determined broad enrichment regions using broadPeak format
write.narrowpeak.binding | Write out determined binding peaks using narrowPeak format
writewig | A function to save a list of chromosome-wise x/y data frames into a WIG file format.