Man pages for kintany/GTExR
Package for GTEx analysis with R scripts

aggregate_countsAggregates reads counts from SNPs to transcript and...
analyze_imbalance_vs_countsReads ratios from the file and calculate gini indexes
analyze_NPC_pulled_clonesRuns analysis for NPCs: pull clones, look at SDs
analyze_NPC_varRuns analysis for NPCs
analyze_rinAnalyze rin vs. sd for all individuals for a given tissue
analyze_sd_by_thresholdReads counts, apply thresholds, plot distributions
analyze_sd_for_tissuesAnalyze sd distributions for all individuals for all tissues
analyze_sd_MAE_BAEReads ratios from the file and analyze standard deviations
compare_high_vs_low_samplesCompares sample with high and low ratio variability
compare_same_ind_diff_tissuesCompare same individuals in different tissues
generatePlotsGenerate variatility plots for a given tissue
get_ASE_files_listGets a list of files containing ASE information for a given...
get_classificationReturns tissue classification with Ensembl id column
get_counts_for_sampleGets a table with reference and allelic counts for a given...
get_counts_statisticsCalculates mean, sd, CV, CV2 for each gene
get_full_nameGets full tissue name from a short name
get_individuals_subsetOutputs sample ids for individuals with high or low ratios...
get_ratio_sdGet allelic ratio's standard deviation for a tissue,...
get_ratios_sampleGets ratios for a given tissue
get_rin_correlations_for_tissuesProduce plot with RIN vs SD(allelic_ratio) for several...
get_samples_tissuesReads ratios from the file, subsamples and makes a plot
get_sd_ratiosCalcultates SDs for allelic ratios
get_short_nameGets short tissue name from a full name
get_tissue_codeGets tissue code from a short name
list_of_samples_with_ratiosRun ratios analysis for NPCs
load_countsLoads counts from Rda
load_Gtex_dataCoverts GTEx data from 3 files (downloaded from GTEx website)...
make_plot_for_NPCRun ratios analysis for NPCs
measureCalculates CVs for "observed" BAE and all genes from counts...
plot_CV2_vs_meanPlots CV2 versus mean
plot_density_ratio_per_individualReads ratios from the file and makes a plot of density,...
plot_density_ratio_per_individual_all_tissuesPlot ratio densities for all tissues
plot_onePlots boxplots for ranges
plot_twoPlots scatterplots
process_to_countsProccesses GTEx counts and merges counts statistics with...
read_countsReads counts for a given tissue
read_counts_and_calc_ratiosReads counts for a given tissue, aggregates them and puts...
read_counts_and_merge_samplesReads counts for a given tissue, aggregates them and puts...
read_ratiosReads ratios for a given tissue
save_countsReads and saves counts for a given tissue
save_counts_tissues_of_interestSaves counts to files for the tissues of interest
save_Gtex_data_by_tissueSaves selected tissues counts to .Rda files
save_ratiosReads and saves ratios for a given tissue
save_ratios_tissues_of_interestSaves ratios to files for the tissues of interest
simulate_ratiosMakes boxplots for SDs
subset_and_get_ratioPulls data and gets allelic ratios
subsetGtexDataSubsets GTEx ExpressionSet to a given tissue
variation_analysis_for_subsetDo variation analysis for samples with moderate sd values
zscores_heatmapConvert normalized counts to z-scores and plot heatmaps
kintany/GTExR documentation built on July 21, 2018, 7:48 p.m.