# Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

## Documentation for package ‘TransView’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H L M N O P R S T

TransView-package | Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets.

## -- A --

annotatePeaks | Associates peaks to TSS

## -- C --

chromosomes | Class '"DensityContainer"'
chromosomes-method | Class '"DensityContainer"'
class:DensityContainer | Class '"DensityContainer"'
class:TVResults | Class '"TVResults"'
clusters | Class '"TVResults"'
clusters-method | Class '"TVResults"'
cluster_order | Class '"TVResults"'
cluster_order-method | Class '"TVResults"'
collapsed | Class '"DensityContainer"'
collapsed-method | Class '"DensityContainer"'
compression | Class '"DensityContainer"'
compression-method | Class '"DensityContainer"'

## -- D --

data_pointer | Class '"DensityContainer"'
data_pointer-method | Class '"DensityContainer"'
DensityContainer-class | Class '"DensityContainer"'

## -- E --

env | Class '"DensityContainer"'
env-method | Class '"DensityContainer"'
ex_name | Class '"DensityContainer"'
ex_name-method | Class '"DensityContainer"'
ex_name<- | Class '"DensityContainer"'
ex_name<--method | Class '"DensityContainer"'

## -- F --

filtered | Class '"DensityContainer"'
filtered-method | Class '"DensityContainer"'
filtered_reads | Class '"DensityContainer"'
filtered_reads-method | Class '"DensityContainer"'
fmapmass | Class '"DensityContainer"'
fmapmass-method | Class '"DensityContainer"'

## -- G --

gcoverage | Class '"DensityContainer"'
gcoverage-method | Class '"DensityContainer"'
gsize | Class '"DensityContainer"'
gsize-method | Class '"DensityContainer"'
gtf2gr | GTF file parsing

## -- H --

histogram | Histogram of the read distribution
histogram-method | Histogram of the read distribution
histogram-methods | Histogram of the read distribution

## -- L --

lcoverage | Class '"DensityContainer"'
lcoverage-method | Class '"DensityContainer"'
lmaxScore | Class '"DensityContainer"'
lmaxScore-method | Class '"DensityContainer"'
lowqual | Class '"DensityContainer"'
lowqual-method | Class '"DensityContainer"'
lsize | Class '"DensityContainer"'
lsize-method | Class '"DensityContainer"'

## -- M --

macs2gr | Convenience function for MACS output conversion
maxScore | Class '"DensityContainer"'
maxScore-method | Class '"DensityContainer"'
meltPeak | Convenience function which returns a data frame with normalized peak densities suitable for plotting with ggplot2

## -- N --

neg | Class '"DensityContainer"'
neg-method | Class '"DensityContainer"'
nreads | Class '"DensityContainer"'
nreads-method | Class '"DensityContainer"'

## -- O --

origin | Class '"DensityContainer"'
origin-method | Class '"DensityContainer"'

## -- P --

paired | Class '"DensityContainer"'
paired-method | Class '"DensityContainer"'
paired_reads | Class '"DensityContainer"'
paired_reads-method | Class '"DensityContainer"'
parameters | Class '"TVResults"'
parameters-method | Class '"TVResults"'
parseReads | User configurable efficient assembly of read density maps
peak2tss | Changes the peak center to the next TSS according to previous annotation
plotTV | Plot and cluster global read densities
plotTVData | Summarize plotTV results
plotTVData,TVResults | Summarize plotTV results
plotTVData-method | Summarize plotTV results
plotTVData-methods | Summarize plotTV results
pos | Class '"DensityContainer"'
pos-method | Class '"DensityContainer"'
proper_pairs | Class '"DensityContainer"'
proper_pairs-method | Class '"DensityContainer"'

## -- R --

readthrough_pairs | Class '"DensityContainer"'
readthrough_pairs-method | Class '"DensityContainer"'
rmTV | Free space occupied by DensityContainer
rmTV-method | Free space occupied by DensityContainer
rmTV-methods | Free space occupied by DensityContainer

## -- S --

scores_peaks | Class '"TVResults"'
scores_peaks-method | Class '"TVResults"'
scores_rna | Class '"TVResults"'
scores_rna-method | Class '"TVResults"'
show-method | Class '"DensityContainer"'
show-method | Class '"TVResults"'
size | Class '"DensityContainer"'
size-method | Class '"DensityContainer"'
slice1 | Slice read densities from a TransView dataset
slice1-method | Slice read densities from a TransView dataset
slice1-methods | Slice read densities from a TransView dataset
slice1T | Slice read densities of whole transcripts from a TransView DensityContainer
slice1T-method | Slice read densities of whole transcripts from a TransView DensityContainer
slice1T-methods | Slice read densities of whole transcripts from a TransView DensityContainer
sliceN | Slice read densities from a TransView dataset
sliceN-method | Slice read densities from a TransView dataset
sliceN-methods | Slice read densities from a TransView dataset
sliceNT | Slice read densities of whole transcripts from a TransView DensityContainer
sliceNT-method | Slice read densities of whole transcripts from a TransView DensityContainer
sliceNT-methods | Slice read densities of whole transcripts from a TransView DensityContainer
spliced | Class '"DensityContainer"'
spliced-method | Class '"DensityContainer"'
spliced<- | Class '"DensityContainer"'
spliced<--method | Class '"DensityContainer"'
strands | Class '"DensityContainer"'
strands-method | Class '"DensityContainer"'
summaryTV | Class '"TVResults"'
summaryTV-method | Class '"TVResults"'

## -- T --

TransView | Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets.
TVResults-class | Class '"TVResults"'
tvStats | DensityContainer accessor function
tvStats-method | DensityContainer accessor function
tvStats-methods | DensityContainer accessor function