Package: BaalChIP 1.39.0

Citation | Introduction | Standard workflow | Quick start: example 1 (with pre-computed RAF scores) | Quick start: example 1 with more control over the input options | Quick start: example 2 (with gDNA BAM files) | Input data | The sample sheet | The hets files | The gDNA BAM files | Constructing a BaalChIP object | Obtaining allele-specific counts for BAM files | QCfilter: A filter to exclude SNPs in regions of known problematic read alignment | filterIntbias: A simulation-based filtering to exclude SNPs with intrinsic bias | skipScriptRun | Merge allele counts per group | Removing possible homozygous SNPs | Identifying allele-specific binding events | The reference mapping (RM) bias | The relative allele frequency (RAF) bias | Exporting the results | BaalChIP.report | Sumarizing and plotting data | The ENCODE data set | The FAIREseq data set | summaryQC: summary of QC result. | plotQC: Plot filtering results | Plot simulation results | Exporting the table of assayed SNPs and their allelic counts | summaryASB function | Allelic ratios density plot | Retrieving the RM and RAF scores estimated by BaalChIP | Exporting the final ASB results with BaalChIP.report | Bugs/Feature requests | Session Information | References