Quick Start =========== After successfully installing **BIT** and configuring the reference ChIP-seq database, you are ready to use **BIT** for your analyses. The process is straightforward if you have any of the following file types indicating the chromosomal start and end positions of your epigenomic regions: `.bed`, `.narrowPeak`, `.broadPeak`, `.bigNarrowPeak` (`.bb`), or `.csv`. Assuming your input file is located at `"file_path/file_name"` (acceptable formats: `.bed`, `.bb`, etc.), and you want to store the output in `"output_path"`, the command below will start a comprehensive comparison of your input regions against all available ChIP-seq reference datasets. It then initiates the **BIT** model using the Gibbs sampler to provide the Bayesian inference of the TR-level BIT score. The output data from each iteration will be saved as an R data object named `"file_name.rds"`. .. code-block:: R > BIT(, "file_path/file_name.bed", "output_path/", show = TRUE, plot_bar = TRUE, N = 5000, bin_width = 1000, genome = "hg38") Loading and mapping peaks to bins... Done loading. Comparing the input regions with the pre-compiled reference ChIP-seq data, using a bin width of 1000 bps... Loading meta table... Starting alignment process... |==================================================| 100% Alignment complete. Starting BIT Gibbs sampler with 5000 iterations... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Gibbs sampling completed. Output data saved as output_path/file_name.rds Loading data from file... Processing theta matrix and TR names... Compiling results... Results saved to output_path/file_name_rank_table.csv BIT process completed. There are several default parameters you can change: .. note:: - **show**: `TRUE` / `FALSE`. Whether to display the ranking table. Default: `TRUE`. - **plot.bar**: `TRUE` / `FALSE`. Whether to plot the top 10 TRs BIT scores in a horizontal bar plot. Default: `TRUE`. - **format**: One of `"bed"`, `"narrowPeak"`, `"broadPeak"`, `"bigNarrowPeak"`, `"csv"`, or `NULL`. Specifies the format of the input file. Default: `NULL`. If set to `NULL`, **BIT** will automatically determine the file format based on its extension. - **N**: Integer. The number of iterations in the Gibbs sampler. Default: `5000`. - **bin_width**: Integer. The width of the bin used to divide the chromatin into non-overlapping bins. Default: `1000`. Only change this if you compile a different reference database. - **burnin**: `NULL` or an integer. Specifies the burn-in period when deriving the Bayesian inference for TR-level parameters. Default: `NULL`, which will use `N/2`. - **genome**: `hg38` or `mm10` for TR ChIP-seq data collected from different genome. We can check the results: .. code-block:: R > Results_Table <- read.csv("output_path/file_name_rank_table.csv") > head(Results_Table,10) TR Theta_i lower upper BIT_score BIT_score_lower BIT_score_upper Rank 1 CTCF -2.010571 -2.011593 -2.009676 0.11809745 0.11799114 0.11819079 1 2 RAD21 -2.028610 -2.031747 -2.025619 0.11623164 0.11590978 0.11653925 2 3 SMC3 -2.110100 -2.120542 -2.100907 0.10811898 0.10711622 0.10900866 3 4 SMC1A -2.181305 -2.193447 -2.170246 0.10144192 0.10034048 0.10245443 4 5 PHF2 -2.222166 -2.633869 -1.990377 0.09777755 0.06699025 0.12021697 5 6 GABPB1 -2.301673 -2.689461 -2.062208 0.09098450 0.06359813 0.11282466 6 7 CHD2 -2.317842 -2.370804 -2.270597 0.08965600 0.08542628 0.09358759 7 8 NFYA -2.353494 -2.396030 -2.313238 0.08678843 0.08347594 0.09003250 8 9 NELFCD -2.371794 -2.476460 -2.276018 0.08534898 0.07752502 0.09312872 9 10 NFYC -2.373795 -2.767204 -2.122314 0.08519290 0.05912233 0.10694685 10