Package index • GAMBLR.results

Other

annotate_hotspots(): Annotate Hotspots.

annotate_maf_triplet(): Annotate MAF with triplet context

annotate_ssm_blacklist(): Annotate SSM with Blacklists

annotate_ssm_motif_context(): Annotate mutations target motif

ashm_rainbow_plot(): ASHM Rainbow Plot

assign_cn_to_ssm(): Assign CN state to SSMs.

calc_mutation_frequency_bin_region(): Calculate Mutation Frequency By Sliding Window.

calc_mutation_frequency_bin_regions(): Mutation counts across sliding windows for multiple regions.

check_gene_expression(): Check Gene Expression.

collate_lymphgen(): Collate Lymphgen.

collate_results(): Collate Results

estimate_purity(): Estimate Purity.

maf_to_custom_track(): Maf To Custom Track.

og_get_gambl_metadata(): Get GAMBL metadata.

populate_tool_results(): Populate Tool Results.

pretty_lymphoplot(): LymphGen feature visualization.

tidy_gene_expression(): Tidy gene Expression.

Functions

get_all_coding_ssm(): Get all Coding SSMs

get_ashm_count_matrix(): Get ASHM Count Matrix.

get_cn_segments(): Get CN Segments.

get_cn_states(): Get CN States.

get_cnv_and_ssm_status(): Get CNV and coding SSM combined status

get_coding_ssm(): Get Coding SSM.

get_coding_ssm_status(): Get Coding SSM Status.

get_combined_sv(): Get Combined SV.

get_gambl_metadata(): Get GAMBL metadata.

get_gambl_outcomes(): Get GAMBL Outcomes.

get_gene_cn_and_expression(): Get Gene CN and Expression.

get_gene_expression(): Get Gene Expression.

get_gene_fusions(): Get gene fusions

get_lymphgen(): Get Lymphgen.

get_manta_sv(): Get Manta SVs

get_raw_expression_counts(): Get Raw Expression Counts

get_ssm_by_regions(): Get SSM By Regions.

get_ssm_by_sample(): Get SSM By Sample.

get_ssm_by_samples(): Get SSM By Samples.

get_timed_mutations(): Load MutationTimeR Results