API for chromVAR
Chromatin Variation Across Regions

Global functions
ProbSampleReplace Source code
addGCBias Man page
addGCBias,RangedSummarizedExperiment-method Man page
addGCBias,SummarizedExperiment-method Man page
all_equal Source code
all_false Source code
all_true Source code
all_whole Source code
annoation_matches<-,SummarizedExperiment-method Man page
annotationMatches Man page
annotationMatches,SummarizedExperiment-method Man page Man page
annotationMatches<- Man page
annotationMatches<-,SummarizedExperiment-method Man page
anova_helper Source code
assembleKmers Man page Source code
bamToFragments Source code
bamToFragmentsByRG Source code
bf_kw_var_test Source code
bf_var_test Source code
bg_sample_helper Source code
bias_skew Source code
cbind,chromVARDeviations-method Man page
chromVAR Man page
chromVAR-package Man page
chromVARDeviations-class Man page
chromVAR_theme Man page Source code
computeDeviations Man page
computeDeviations,MatrixOrmatrix,MatrixOrmatrix-method Man page
computeDeviations,MatrixOrmatrix,SummarizedExperiment-method Man page
computeDeviations,MatrixOrmatrix,list-method Man page
computeDeviations,MatrixOrmatrix,missingOrNULL-method Man page
computeDeviations,SummarizedExperiment,MatrixOrmatrix-method Man page
computeDeviations,SummarizedExperiment,SummarizedExperiment-meth Man page
computeDeviations,SummarizedExperiment,list-method Man page
computeDeviations,SummarizedExperiment,missingOrNULL-method Man page
computeExpectations Man page
computeExpectations,MatrixOrmatrix-method Man page
computeExpectations,SummarizedExperiment-method Man page
computeVariability Man page Source code
compute_deviations_core Source code
compute_deviations_single Source code
compute_expectations_core Source code
compute_pwm_dist Source code
compute_pwm_dist2 Source code
compute_variability_single Source code
convert_from_ix_list Source code
convert_to_ix_list Source code
counts,SummarizedExperiment-method Man page
counts<-,SummarizedExperiment,MatrixOrmatrix-method Man page
counts<-,SummarizedExperiment-method Man page
counts_check Source code
deviationScores Man page
deviationScores,chromVARDeviations-method Man page Man page
deviations Man page
deviations,chromVARDeviations-method Man page Man page
deviationsCovariability Man page Source code
deviationsTsne Man page Source code
deviations_tsne_inv_shiny Source code
deviations_tsne_shiny Source code
differentialDeviations Man page Source code
differentialVariability Man page Source code
euc_dist Source code
example_counts Man page
expected_n_overlap_kmers Source code
filterPeaks Man page Source code
filterSamples Man page Source code
filterSamplesPlot Man page Source code
filter_samples_gadget Source code
getAnnotationCorrelation Man page
getAnnotationCorrelation,MatrixOrmatrix,MatrixOrmatrix-method Man page
getAnnotationCorrelation,MatrixOrmatrix,SummarizedExperiment-met Man page
getAnnotationCorrelation,MatrixOrmatrix,list-method Man page
getAnnotationCorrelation,SummarizedExperiment,MatrixOrmatrix-met Man page
getAnnotationCorrelation,SummarizedExperiment,SummarizedExperime Man page
getAnnotationCorrelation,SummarizedExperiment,list-method Man page
getAnnotationCorrelation_core Source code
getAnnotationSynergy Man page
getAnnotationSynergy,MatrixOrmatrix,MatrixOrmatrix-method Man page
getAnnotationSynergy,MatrixOrmatrix,SummarizedExperiment-method Man page
getAnnotationSynergy,MatrixOrmatrix,list-method Man page
getAnnotationSynergy,SummarizedExperiment,MatrixOrmatrix-method Man page
getAnnotationSynergy,SummarizedExperiment,SummarizedExperiment-m Man page
getAnnotationSynergy,SummarizedExperiment,list-method Man page
getAnnotationSynergy_core Source code
getAnnotations Man page
getAnnotations,GRangesList-method Man page
getAnnotations,MatrixOrmatrix-method Man page
getAnnotations,character-method Man page
getAnnotations,data.frame-method Man page
getAnnotations,list-method Man page
getBackgroundPeaks Man page
getBackgroundPeaks,MatrixOrmatrix-method Man page
getBackgroundPeaks,RangedSummarizedExperiment-method Man page
getBackgroundPeaks,SummarizedExperiment-method Man page
getCisGroups Man page
getCisGroups,GenomicRanges-method Man page
getCisGroups,RangedSummarizedExperiment-method Man page
getCounts Man page Source code
getFragmentCountsByRG Source code
getFragmentsPerPeak Man page
getFragmentsPerPeak,MatrixOrmatrix-method Man page
getFragmentsPerPeak,SummarizedExperiment-method Man page
getFragmentsPerSample Man page
getFragmentsPerSample,MatrixOrmatrix-method Man page
getFragmentsPerSample,SummarizedExperiment-method Man page
getJasparMotifs Man page Source code
getPeaks Man page Source code
getPermutedData Man page Source code
getSampleCorrelation Man page Source code
getSampleDepths Man page Source code
getSampleDepthsByRG Source code
getSampleDistance Man page Source code
getTotalFragments Man page
getTotalFragments,MatrixOrmatrix-method Man page
getTotalFragments,SummarizedExperiment-method Man page
get_background_peaks_alternative Source code
get_background_peaks_core Source code
get_cis_groups_core Source code
get_cor_helper Source code
get_counts_from_bams Source code
get_counts_from_beds Source code
get_covariable_kmers Source code
get_jaccard Source code
get_kmer_dist Source code
get_kmer_positions Source code
get_mm_kmers Source code
get_null_kmer_dist Source code
get_overlap_kmers Source code
get_permuted_data_helper Source code
get_reverse_complement Source code
get_sample_depths_from_bams Source code
get_sample_depths_from_beds Source code
get_variability_boost_helper Source code
getstrand Source code
is.installed Source code
kmer_group_to_pwm Source code
kmers_to_names Source code
kw_helper Source code
last_element Source code
left_right_to_grglist Source code
makeBiasBins Man page
makeBiasBins,MatrixOrmatrix-method Man page
makeBiasBins,RangedSummarizedExperiment-method Man page
makeBiasBins,SummarizedExperiment-method Man page
makeBiasBins_core Source code
makePermutedSets Man page
makePermutedSets,MatrixOrmatrix,MatrixOrmatrix-method Man page
makePermutedSets,MatrixOrmatrix,SummarizedExperiment-method Man page
makePermutedSets,MatrixOrmatrix,list-method Man page
makePermutedSets,RangedSummarizedExperiment,MatrixOrmatrix-metho Man page
makePermutedSets,RangedSummarizedExperiment,SummarizedExperiment Man page
makePermutedSets,RangedSummarizedExperiment,list-method Man page
makePermutedSets,SummarizedExperiment,MatrixOrmatrix-method Man page
makePermutedSets,SummarizedExperiment,SummarizedExperiment-metho Man page
makePermutedSets,SummarizedExperiment,list-method Man page
makePermutedSets_core Source code
matchKmers Man page
matchKmers,DNAString,ANY-method Man page
matchKmers,DNAStringSet,ANY-method Man page
matchKmers,character,DNAString-method Man page
matchKmers,character,DNAStringSet-method Man page
matchKmers,character,GenomicRanges-method Man page
matchKmers,character,RangedSummarizedExperiment-method Man page
matchKmers,character,character-method Man page
matchKmers,numeric,ANY-method Man page
match_kmers_helper Source code
match_kmers_inner_helper Source code
matches_check Source code
mean_smooth Source code
means.along Source code
merge_lists Source code
mini_counts Man page
mini_dev Man page
mini_ix Man page
mxsort Source code
onUnload Source code
pfm_to_prob_helper Source code
plotDeviationsTsne Man page Source code
plotKmerMismatch Man page Source code
plotVariability Man page Source code
plot_deviations_tsne_shiny Source code
pwmDistance Man page Source code
pwm_dist_single Source code
pwm_euclidean Source code
pwm_to_prob Source code
pwm_to_prob_helper Source code
pwm_type Source code
quantile_helper Source code
rbind,chromVARDeviations-method Man page
readAlignmentFromBed Source code
readNarrowpeaks Man page Source code
remove_correlated_helper Source code
remove_nonoverlap Source code
remove_overlap Source code
remove_rc Source code
reorder_columns Source code
rms Source code
row_sds Source code
row_sds_perm Source code
sd.along Source code
seq_to_pwm Source code
split_alpha_numeric Source code
t_helper Source code
tabulate2 Source code
toIC Source code
upper_bias_limit_helper Source code
variability_table Source code
wilcoxon_helper Source code
zero_or_null Source code
chromVAR documentation built on Nov. 17, 2017, 10:14 a.m.