Man pages for TeamMacLean/atacr
Analysing Capture Seq Count Data

as.data.frame.atacrreturns dataframe of data in atacr object
as.matrix.atacrreturns given subset of data in atacr object as a matrix
assay_matrix_to_dfconverts SummarizedExperiment::assay matrix to a dataframe...
bootstrap_truns bootstrap t test, wrapper required for boot::boot...
calc_quantilesreport counts at each quantile for each sample
chromosome_coveragePlot density of read counts by sample over the chromosomes
control_window_normaliseperforms control window based normalisation of the selected...
control_window_normalise_internaldo a control window scaling normalisation
control_window_scaling_factorsextract scaling factors from control windows (often from a...
count_windows_under_thresholdcount windows that have read counts below the threshold
coverage_count_summaryGet a summary of depth of coverage in the bait and non bait...
coverage_summaryPlot histograms of read counts by sample and window type
Est.DepthDepth estimation, directly from...
estimate_bayes_factorEstimate Bayes Factor and significantly different windows
estimate_bayes_factor_multiclassEstimate BayesFactor and mark significantly different windows...
estimate_fdrEstimate FDR and significantly different windows
estimate_fdr_multiclassEstimate FDR and significantly different windows for many...
estimate_GoFsestimates Goodness of Fit from atacr object
extract_features_from_gffpulls lines out of a gff file based on identifierss provided
find_controls_by_GoFfind control windows by convergence method in...
get_bait_regions_from_gffreads a gff file containing the bait regions
get_bait_regions_from_textreads a csv file containing the bait regions
get_expected_valuesgiven a vector of values return a set of random numbers from...
get_GoF_factorsestimates sequencing depths based on windows with smallest...
get_tgets t-statistic for two vectors of data, x and y
gofestimates Goodness of Fit for each row in a count matrix
library_size_normalisationperforms a whole library size normalisation of the selected...
library_size_normalisation_internaldo a library size normalisation
library_size_scaling_factorscalculate scaling factors for library size
load_atacpopulate the result object with the...
load_rnaseqpopulate the result object with the...
ma_dataadds an 'm' and an 'a' column to an assay matrix dataframe...
make_corrplotgenerate corrplot from matrix of counts
make_countsload BAM files and calculate window coverage
make_csaw_paramsformat a csaw::readParam object from the atacr::make_params()...
make_paramsset read filters for counting from the BAM file.
make_scanBamParamformat a rsamtools::scanBam object from the...
make_UpSetRgiven a dataframe from the estimate_fdr_multiclass()...
ma_plotplot M (log2 ratio of a windows sample count to windows...
median_virtual_experimenta median of window values across all samples in a vector, for...
normalise_by_window_widthnormalise counts by window width (counts / window width)
observed_expected_binsgiven a vector of numbersd returns the counts in bins of...
plot.atacrreturns summary plot of data in atacr object
plot_count_by_chromosomeplot the counts split by chromosome and sample
plot_countsPlot distribution of counts in given data set
plot_GoFdraw count distribution of GOF estimates
print.atacrwrites a summary of the metadata for a given atacr object
qqarbNamed distribution qqplot
read_experiment_infoLoads in a CSV file describing treatment, samples and bam...
sample_correlation_plotPlot sample count correlations
sample_kmeans_clusteridentify kmeans clusters for samples
scale_factor_normalisenormalise by a provided set of scaling factors
select_dataselects appropriate columns and names from a
sim_countssim_counts - simulated count data
simulate_countssimulate counts and return an atacr object
small_countssmall_counts - simulated count data The data 'small_counts'...
summary.atacrwrites a detailed data summary of the atacr object
target_count_coverageRead count and mean coverage hitting the bait and non bait...
target_count_summaryGet a summary of reads hitting the bait and non bait windows
treatmentsreturn list of treatment names
view_genecoverage over gene model
windows_below_coverage_threshold_plotgenerate cumulative plot of number of windows below a...
TeamMacLean/atacr documentation built on Nov. 8, 2017, 12:05 a.m.