R/zzz.R
In ndbrown6/MSK-GRAIL-TECHVAL: High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
snv_file <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scored_merged_snvs_20171115.tsv"
)
)
indel_file <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scored_merged_indels_20171115.tsv"
)
)
hypermutators <- list(
patient_id = c(
"MSK-VB-0023",
"MSK-VB-0044",
"MSK-VB-0046",
"MSK-VB-0050",
"MSK-VB-0057",
"MSK-VL-0035",
"MSK-VL-0054",
"MSK-VP-0031",
"MSK-VP-0054"
)
)
msi_hypermutators <- list(
patient_id = c(
"MSK-VP-0041"
)
)
common_bed <- str_c(
"../",
"modified_v11/",
"Resources/",
"Bed_files/",
"pan_v2_wo_decoy_wo_iSNP_wo_CNV_IMPACT_common_regions.merged.bed"
)
common_bed_annotated <- str_c(
"../",
"modified_v11/",
"Resources/",
"Bed_files/",
"pan_v2_wo_decoy_wo_iSNP_wo_CNV_IMPACT_common_regions.merged_annotated.bed"
)
common_bed_annotated_w_introns <- str_c(
"../",
"modified_v11/",
"Resources/",
"Bed_files/",
"pan_v2_wo_decoy_wo_iSNP_wo_CNV_IMPACT_common_regions.merged_annotated_w_introns.bed"
)
patient_tracker <- str_c(
"../",
"modified_v11/",
"Tracker_files/",
"s3_sample_tracker_TechVal_Merlin.csv"
)
impact_tracker <- str_c(
"../",
"modified_v11/",
"Tracker_files/",
"sample_tracker_IMPACT_BAM_20170227.csv"
)
wbc_variants <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Stacked_Scored_WBC/",
"wbc_scored_annotated.tsv"
),
annotations = str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"wbc_scored_annotated.maf"
)
)
clinical_file <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"clinical_no_dates_1_201703241549.tsv"
)
clinical_file_updated <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"clinical_no_dates_1_201703241549_updated.tsv"
)
somatic_vars_breast <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"IMPACT_annotated_variants/",
"normal_silent_common_intron_target.tables_merged_breast.tsv"
)
somatic_vars_lung <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"IMPACT_annotated_variants/",
"normal_silent_common_intron_target.tables_merged_lung.tsv"
)
somatic_vars_prostate <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"IMPACT_annotated_variants/",
"normal_silent_common_intron_target.tables_merged_prostate.tsv"
)
cosmic_v84 <- str_c(
"../",
"modified_v11/",
"Resources/",
"External_database/",
"cosmic_v84.tsv"
)
gnomad_r2.0.1 <- str_c(
"../",
"modified_v11/",
"Resources/",
"External_database/",
"gnomad_r2.0.1.tsv"
)
hotspot_v2 <- str_c(
"../",
"modified_v11/",
"Resources/",
"External_database/",
"cancer_hotspots_v2.tsv"
)
wbc_scored_annotated_and_clinical <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Stacked_Scored_WBC/",
"wbc_scored_annotated_280519.tsv"),
clinical = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Stacked_Scored_WBC/",
"clinical_280519.tsv")
)
chip_genes <- c(
"DNMT3A",
"TET2",
"ASXL1",
"PPM1D",
"TP53",
"JAK2",
"RUNX1",
"SF3B1",
"SRSF2",
"IDH1",
"IDH2",
"U2AF1",
"CBL",
"ATM",
"CHEK2"
)
somatic_snvs_grail <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scored_merged_snvs_20171115.tsv"
)
)
somatic_indels_grail <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scored_merged_indels_20171115.tsv"
)
)
msk_anno_joined <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scripts2/",
"20180412_MSK_TechVal_Grail_small_variants_bio_source_label.filter_vus_biopsy_only.all_cases_ccf.tsv"
)
url_techval.repeats <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"annotated.tsv"
)
url_ddpcr <- str_c(
"https://",
"docs.google.com/",
"spreadsheets/",
"d/",
"1s9PKGYZ1v3vgUiC25N6D5jXX1ai6c0vbisZsKIgwGlg/",
"edit?usp=sharing"
)
url_retest <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Stacked_annotated_retest/",
"TechVal_retest_annotated_stack.tsv"
)
url_cell.line <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Titrations_cell_line/",
"scored/",
"annotated.tsv"
)
url_HD753.truth <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Titrations_cell_line/",
"hd753_manifest.tsv"
)
url_qc.metrics <- str_c(
"../",
"modified_v11/",
"QC_metrics/",
"TechVal_Merlin_QC_metrics.tsv"
)
url_ctdna_frac <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"ctDNA_fraction.csv"
)
url_volumetric_data <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"Volumetric_data.xls"
)
url_psa <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"PSA_MSK_VP_0041.txt"
)
url_recist <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"RECIST_MSK_VP_0041.txt"
)
url_msi_processed_data <- str_c(
"../",
"modified_v11/",
"MSIMSK/",
"data/",
"20180423_msi_global_df.tsv"
)
url_subject_alias <- str_c(
"../",
"modified_v11/",
"MSIMSK/",
"data/",
"MSK_TechVal_MS_patient_ID_alias_mapping.tsv"
)
url_prior_tx <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"prior_tx_techval_0818.txt"
)
url_master_key <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"master_sample_key.tsv"
)
url_cytogenetic_data <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"hg19_cytoBandIdeo.txt"
)
url_leftover_samples <- str_c(
"../",
"modified_v11/",
"Resources/",
"ddPCR/",
"msk_techval_ddpcr_samples.tsv"
)
url_ddpcr_results <- str_c(
"../",
"modified_v11/",
"Resources/",
"ddPCR/",
"msk_techval_ddprc_results.csv"
)
url_smoking_history <- list(
breast = str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"MSK_VB_SMOKING.csv"
),
prostate = str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"MSK_VP_SMOKING.csv"
)
)
url_guardant_g360 <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"Guardant360_gene_list.tsv"
)
url_sample.tracker <- patient_tracker
url_msk.snv <- snv_file$scored
url_msk.indel <- indel_file$scored
germline_alpha <- 0.15
bam_read_count_cutoff <- 2
ad_cutoff <- 5
ref_genome <- BSgenome.Hsapiens.UCSC.hg19
url_original <- url_msk.snv
url_target.bed <- common_bed
cohort_cols <- c(
"Control" = "#0063AA",
"Breast" = "#EF145D",
"Lung" = "#F98450",
"Prostate" = "#009700"
)
variant_cols <- c(
"VUSo" = "#4E9B3C",
"biopsy_matched" = "#2C80C3",
"IMPACT-BAM_matched" = "#F9CA03",
"WBC_matched" = "#EA7180",
"biopsy_only" = "#2C80C3"
)
ndbrown6/MSK-GRAIL-TECHVAL documentation built on March 29, 2020, 4:41 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
snv_file <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scored_merged_snvs_20171115.tsv"
)
)
indel_file <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scored_merged_indels_20171115.tsv"
)
)
hypermutators <- list(
patient_id = c(
"MSK-VB-0023",
"MSK-VB-0044",
"MSK-VB-0046",
"MSK-VB-0050",
"MSK-VB-0057",
"MSK-VL-0035",
"MSK-VL-0054",
"MSK-VP-0031",
"MSK-VP-0054"
)
)
msi_hypermutators <- list(
patient_id = c(
"MSK-VP-0041"
)
)
common_bed <- str_c(
"../",
"modified_v11/",
"Resources/",
"Bed_files/",
"pan_v2_wo_decoy_wo_iSNP_wo_CNV_IMPACT_common_regions.merged.bed"
)
common_bed_annotated <- str_c(
"../",
"modified_v11/",
"Resources/",
"Bed_files/",
"pan_v2_wo_decoy_wo_iSNP_wo_CNV_IMPACT_common_regions.merged_annotated.bed"
)
common_bed_annotated_w_introns <- str_c(
"../",
"modified_v11/",
"Resources/",
"Bed_files/",
"pan_v2_wo_decoy_wo_iSNP_wo_CNV_IMPACT_common_regions.merged_annotated_w_introns.bed"
)
patient_tracker <- str_c(
"../",
"modified_v11/",
"Tracker_files/",
"s3_sample_tracker_TechVal_Merlin.csv"
)
impact_tracker <- str_c(
"../",
"modified_v11/",
"Tracker_files/",
"sample_tracker_IMPACT_BAM_20170227.csv"
)
wbc_variants <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Stacked_Scored_WBC/",
"wbc_scored_annotated.tsv"
),
annotations = str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"wbc_scored_annotated.maf"
)
)
clinical_file <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"clinical_no_dates_1_201703241549.tsv"
)
clinical_file_updated <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"clinical_no_dates_1_201703241549_updated.tsv"
)
somatic_vars_breast <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"IMPACT_annotated_variants/",
"normal_silent_common_intron_target.tables_merged_breast.tsv"
)
somatic_vars_lung <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"IMPACT_annotated_variants/",
"normal_silent_common_intron_target.tables_merged_lung.tsv"
)
somatic_vars_prostate <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"IMPACT_annotated_variants/",
"normal_silent_common_intron_target.tables_merged_prostate.tsv"
)
cosmic_v84 <- str_c(
"../",
"modified_v11/",
"Resources/",
"External_database/",
"cosmic_v84.tsv"
)
gnomad_r2.0.1 <- str_c(
"../",
"modified_v11/",
"Resources/",
"External_database/",
"gnomad_r2.0.1.tsv"
)
hotspot_v2 <- str_c(
"../",
"modified_v11/",
"Resources/",
"External_database/",
"cancer_hotspots_v2.tsv"
)
wbc_scored_annotated_and_clinical <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Stacked_Scored_WBC/",
"wbc_scored_annotated_280519.tsv"),
clinical = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Stacked_Scored_WBC/",
"clinical_280519.tsv")
)
chip_genes <- c(
"DNMT3A",
"TET2",
"ASXL1",
"PPM1D",
"TP53",
"JAK2",
"RUNX1",
"SF3B1",
"SRSF2",
"IDH1",
"IDH2",
"U2AF1",
"CBL",
"ATM",
"CHEK2"
)
somatic_snvs_grail <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scored_merged_snvs_20171115.tsv"
)
)
somatic_indels_grail <- list(
scored = str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scored_merged_indels_20171115.tsv"
)
)
msk_anno_joined <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"scripts2/",
"20180412_MSK_TechVal_Grail_small_variants_bio_source_label.filter_vus_biopsy_only.all_cases_ccf.tsv"
)
url_techval.repeats <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Joined_cfDNA_IMPACT_variants/",
"annotated.tsv"
)
url_ddpcr <- str_c(
"https://",
"docs.google.com/",
"spreadsheets/",
"d/",
"1s9PKGYZ1v3vgUiC25N6D5jXX1ai6c0vbisZsKIgwGlg/",
"edit?usp=sharing"
)
url_retest <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Stacked_annotated_retest/",
"TechVal_retest_annotated_stack.tsv"
)
url_cell.line <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Titrations_cell_line/",
"scored/",
"annotated.tsv"
)
url_HD753.truth <- str_c(
"../",
"modified_v11/",
"Variants_Calls/",
"Titrations_cell_line/",
"hd753_manifest.tsv"
)
url_qc.metrics <- str_c(
"../",
"modified_v11/",
"QC_metrics/",
"TechVal_Merlin_QC_metrics.tsv"
)
url_ctdna_frac <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"ctDNA_fraction.csv"
)
url_volumetric_data <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"Volumetric_data.xls"
)
url_psa <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"PSA_MSK_VP_0041.txt"
)
url_recist <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"RECIST_MSK_VP_0041.txt"
)
url_msi_processed_data <- str_c(
"../",
"modified_v11/",
"MSIMSK/",
"data/",
"20180423_msi_global_df.tsv"
)
url_subject_alias <- str_c(
"../",
"modified_v11/",
"MSIMSK/",
"data/",
"MSK_TechVal_MS_patient_ID_alias_mapping.tsv"
)
url_prior_tx <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"prior_tx_techval_0818.txt"
)
url_master_key <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"master_sample_key.tsv"
)
url_cytogenetic_data <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"hg19_cytoBandIdeo.txt"
)
url_leftover_samples <- str_c(
"../",
"modified_v11/",
"Resources/",
"ddPCR/",
"msk_techval_ddpcr_samples.tsv"
)
url_ddpcr_results <- str_c(
"../",
"modified_v11/",
"Resources/",
"ddPCR/",
"msk_techval_ddprc_results.csv"
)
url_smoking_history <- list(
breast = str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"MSK_VB_SMOKING.csv"
),
prostate = str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"MSK_VP_SMOKING.csv"
)
)
url_guardant_g360 <- str_c(
"../",
"modified_v11/",
"Resources/",
"MSK_additional_data/",
"Guardant360_gene_list.tsv"
)
url_sample.tracker <- patient_tracker
url_msk.snv <- snv_file$scored
url_msk.indel <- indel_file$scored
germline_alpha <- 0.15
bam_read_count_cutoff <- 2
ad_cutoff <- 5
ref_genome <- BSgenome.Hsapiens.UCSC.hg19
url_original <- url_msk.snv
url_target.bed <- common_bed
cohort_cols <- c(
"Control" = "#0063AA",
"Breast" = "#EF145D",
"Lung" = "#F98450",
"Prostate" = "#009700"
)
variant_cols <- c(
"VUSo" = "#4E9B3C",
"biopsy_matched" = "#2C80C3",
"IMPACT-BAM_matched" = "#F9CA03",
"WBC_matched" = "#EA7180",
"biopsy_only" = "#2C80C3"
)
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