Man pages for TeamMacLean/atacr
Analysing Capture Seq Count Data
| as.data.frame.atacr | returns dataframe of data in atacr object |
| as.DGEList | returns DGEList for edgeR from atacr object |
| as.matrix.atacr | returns given subset of data in atacr object as a matrix |
| assay_matrix_to_df | converts SummarizedExperiment::assay matrix to a dataframe... |
| athal_wt_counts | athal_wt_counts - real capture RNASeq count data The data... |
| bootstrap_t | runs bootstrap t test, wrapper required for boot::boot... |
| calc_quantiles | report counts at each quantile for each sample |
| chromosome_coverage | Plot density of read counts by sample over the chromosomes |
| control_window_normalise | performs control window based normalisation of the selected... |
| control_window_normalise_internal | do a control window scaling normalisation |
| control_window_scaling_factors | extract scaling factors from control windows (often from a... |
| count_windows_under_threshold | count windows that have read counts below the threshold |
| coverage_count_summary | Get a summary of depth of coverage in the bait and non bait... |
| coverage_summary | Plot histograms of read counts by sample and window type |
| edgeR_exact | Estimate differential window counts and mark significantly... |
| edgeR_multiclass | Estimate differential window counts and mark significantly... |
| Est.Depth | Depth estimation, directly from... |
| estimate_bayes_factor | Estimate Bayes Factor and significantly different windows |
| estimate_bayes_factor_multiclass | Estimate BayesFactor and mark significantly different windows... |
| estimate_fdr | Estimate FDR and significantly different windows |
| estimate_fdr_multiclass | Estimate FDR and significantly different windows for many... |
| estimate_GoFs | estimates Goodness of Fit from atacr object |
| extract_features_from_gff | pulls lines out of a gff file based on identifierss provided |
| find_controls_by_GoF | find control windows by convergence method in... |
| get_bait_regions_from_gff | reads a gff file containing the bait regions |
| get_bait_regions_from_text | reads a csv file containing the bait regions |
| get_expected_values | given a vector of values return a set of random numbers from... |
| get_GoF_factors | estimates sequencing depths based on windows with smallest... |
| get_t | gets t-statistic for two vectors of data, x and y |
| gof | estimates Goodness of Fit for each row in a count matrix |
| library_size_normalisation | performs a whole library size normalisation of the selected... |
| library_size_normalisation_internal | do a library size normalisation |
| library_size_scaling_factors | calculate scaling factors for library size |
| load_atac | populate the result object with the... |
| load_rnaseq | populate the result object with the... |
| ma_data | adds an 'm' and an 'a' column to an assay matrix dataframe... |
| make_corrplot | generate corrplot from matrix of counts |
| make_counts | load BAM files and calculate window coverage |
| make_csaw_params | format a csaw::readParam object from the atacr::make_params()... |
| make_params | set read filters for counting from the BAM file. |
| make_scanBamParam | format a rsamtools::scanBam object from the... |
| make_tutorial_data | make data to follow on in the tutorial |
| make_UpSetR | given a dataframe from the estimate_fdr_multiclass()... |
| ma_plot | plot M (log2 ratio of a windows sample count to windows... |
| median_virtual_experiment | a median of window values across all samples in a vector, for... |
| normalise_by_window_width | normalise counts by window width (counts / window width) |
| observed_expected_bins | given a vector of numbersd returns the counts in bins of... |
| plot.atacr | returns summary plot of data in atacr object |
| plot_count_by_chromosome | plot the counts split by chromosome and sample |
| plot_counts | Plot distribution of counts in given data set |
| plot_GoF | draw count distribution of GOF estimates |
| print.atacr | writes a summary of the metadata for a given atacr object |
| qqarb | Named distribution qqplot |
| read_experiment_info | Loads in a CSV file describing treatment, samples and bam... |
| sample_correlation_plot | Plot sample count correlations |
| sample_kmeans_cluster | identify kmeans clusters for samples |
| sample_pca_plot | PCA plot of samples |
| scale_factor_normalise | normalise by a provided set of scaling factors |
| select_data | selects appropriate columns and names from a |
| sim_counts | sim_counts - simulated count data |
| simulate_counts | simulate counts and return an atacr object |
| small_counts | small_counts - simulated count data The data 'small_counts'... |
| summary.atacr | writes a detailed data summary of the atacr object |
| target_count_coverage | Read count and mean coverage hitting the bait and non bait... |
| target_count_summary | Get a summary of reads hitting the bait and non bait windows |
| text_to_gff | writes GFF3 version of a simple text file describing the bait... |
| treatments | return list of treatment names |
| view_gene | coverage over gene model |
| windows_below_coverage_threshold_plot | generate cumulative plot of number of windows below a... |
