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


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Documentation for package ‘TransView’ version 1.10.0

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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