Package index • chromTFR

Datasets and insertion sites

Reading a ChrAccR dataset and turning fragments into Tn5 cuts.

loadAccDataset(): Load a ChrAccR dataset

getAccSamples(): Sample identifiers of a ChrAccR dataset

getAccSampleAnnotation(): Sample annotation of a ChrAccR dataset

getAccRegions(): Region set of a ChrAccR dataset

getTn5Insertions(): Tn5 insertion sites of one sample

mergeInsertionSites(): Pool the insertion sites of several samples

makeInsertionReader(): Per sample reader for runChromTFR

Profiles and deviation scores

Footprint profiles, the GC expected model and the deviation score.

prepareTFBS(): Prepare the binding sites of one motif

accProfile(): Insertion profile around a set of binding sites

accDeviationScore(): Central over flanking insertion density

accDeviation(): Deviation of an observed and expected profile pair

addGCBintoAccessome(): Insertion density of each GC bin

computeAccExpectations(): Expected insertion profile from the GC composition

computeAccDeviation(): Bias corrected deviation of one motif

computeRowZScore(): Row-wise z-score of a matrix

runChromTFR(): Deviation scores of a ChrAccR dataset

Tn5 k-mer bias

The sequence based expected model.

kmerBackground(): Count the k-mers of the accessible genome

computeKmerBias(): Tn5 sequence preference of one sample

kmerBiasProfile(): Expected cut propensity along a set of binding sites

kmerIndexProfile(): k-mer identities along a set of binding sites

profileFromBias(): Expected profile of one sample from stored k-mer identities

scaleToFlank(): Match an expected profile to the flanks of an observed one

Footprint figures

accFootprintData(): Footprint data of one motif across groups

accRawPanel(): Observed against expected footprint panel

accDiffPanel(): Bias corrected footprint panel

plotAccFootprintGrid(): Grid of footprint panels

plotExpectedAccFootprint(): Observed and expected profile of one motif in one sample

plotAccMotifFootprint(): Bias corrected footprint of one motif

Deviation heatmap

accObservedMatrix(): Observed deviation of every motif in every sample

accExpectedMatrix(): Expected deviation of every motif in every sample

plotAccDeviationHeatmap(): Heatmap of bias corrected deviation z-scores