config.R

# (required) the following paths indicate the location of the project (PROJECT_PATH) and the location of where files should be written (OUTPUT PATH)
OUTPUT_PATH = '/fh/fast/matsen_e/shared/tcr-gwas/mechanistic-trimming/motif_data'
PROJECT_PATH = '/home/mrussel2/mechanistic-trimming'

# (optional) Parsed TCR repertoire data (data located within the `emerson_parsed_TCRB.tgz` file available at https://doi.org/10.5281/zenodo.5719520)
TCR_REPERTOIRE_DATA_parsimony = paste0(PROJECT_PATH, '/_ignore/emerson_stats/')
# (required) Training data set; change the path to these data after IGoR processing
TCR_REPERTOIRE_DATA_igor = paste0(PROJECT_PATH, '/_ignore/emerson_igor_stats/')

# (required) TRB gene names and germline sequences from IMGT
WHOLE_NUCSEQS_igor = paste0(PROJECT_PATH,'/_ignore/igor_imgt_genes.tsv')

# (optional) Other gene name and germline sequences for other loci
WHOLE_NUCSEQS_parsimony = paste0(PROJECT_PATH,'/_ignore/tcrb_processed_geneseq.tsv')
WHOLE_NUCSEQS_alpha = paste0(PROJECT_PATH,'/_ignore/imgt_tcra_sequences.tsv')
WHOLE_NUCSEQS_gamma = paste0(PROJECT_PATH, '/_ignore/imgt_tcrg_sequences.tsv')
WHOLE_NUCSEQS_delta = paste0(PROJECT_PATH,'/_ignore/imgt_tcrd_sequences.tsv') 
WHOLE_NUCSEQS_igh = paste0(PROJECT_PATH,'/_ignore/imgt_igh_sequences.tsv')

# (optional) SNP genotype file (download https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001918.v1.p1)
SNP_GDS_FILE <<- paste0(PROJECT_PATH, "/_ignore/HSCT_comb_geno_combined_v03_tcr.gds")

# (optional) File to map scanIDs to localID (data located within the `gwas_id_mapping.tsv` file available at https://doi.org/10.5281/zenodo.5719520)
ID_MAPPING_FILE <<- paste0(PROJECT_PATH, '/_ignore/gwas_id_mapping.tsv')