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ProGeM_settings.r
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######################################## USER-DEFINED SETTINGS ########################################
## 1. DIRECTORIES AND FILES
# Working directory:
base_dir <- ""
# Output directory:
output_dir <- "" # this can be the same as
# base_dir
# Directory for GTEx eQTL data set:
eQTLdata_dir <- ""
# File containing a curated list of known metabolic phenotype-related genes:
filename_metabolic_genes <- "annotated_metabolic_genes.RData" # default provided.
# File containing reference genes:
gene_model_filename <- "GRCh37_genes.RData" # default provided.
# Files containing GWAS sentinel and proxy variants:
sentinel_filename <- "sentinel_information.txt" # user provided (in 'base_dir').
proxy_filename <- "proxy_information.txt" # user provided (in 'base_dir').
# File containing VEP annotation:
VEP_filename <- "VEP_output.txt" # user provided (in 'base_dir').
#------------------------------------------------------------------------------------------------------
## 2. PARAMETERS FOR TOP-DOWN APPROACH
# Set filter for proxy variants based on r2 values:
filtering_required <- TRUE # TRUE or FALSE.
# If TRUE, set threshold for r2 values:
r2_thresh <- 0.8 # default is 0.8.
# Genomic interval (in kb) either side of the sentinel SNP:
interval_kb <- 500 # default is 500kb.
#------------------------------------------------------------------------------------------------------
## 3. PARAMETERS FOR BOTTOM-UP APPROACH
# Genomic interval (in kb) of the overhang of the left-most and right-most proxy/sentinel variant at
# each locus:
LD_region_overhang_kb <- 5 # default is 5kb.
# Number of nearest genes that reside nearest to the sentinel variant:
number_of_nearest <- 3 # default is 3.
# Biotype(s) of candidate genes:
# further information: http://vega.archive.ensembl.org/info/about/gene_and_transcript_types.html
biotype_of_interest <- "protein_coding" # default is "protein_coding".
# Column indices in the VEP output that contain the following information:
sentinel_rsID_column <-
proxy_rsID_column <-
ensembl_gene_id_column <-
IMPACT_column <-
r2_column <- NULL # OPTIONAL: only required if your VEP output needs to be filtered based on r2_thresh
# Tissue(s) of interest for GTEx eQTL data set:
GTEx_tissues <- dir(eQTLdata_dir)[grep("signifpairs", dir(eQTLdata_dir))] # variable contains filenames
# for all GTEx v7 tissues (n=44)
# as per below.
# [1] "Adipose_Subcutaneous.signifpairs.txt"
# [2] "Adipose_Visceral_Omentum.signifpairs.txt"
# [3] "Adrenal_Gland.signifpairs.txt"
# [4] "Artery_Aorta.signifpairs.txt"
# [5] "Artery_Coronary.signifpairs.txt"
# [6] "Artery_Tibial.signifpairs.txt"
# [7] "Brain_Amygdala.signifpairs.txt"
# [8] "Brain_Anterior_cingulate_cortex_BA24.signifpairs.txt"
# [9] "Brain_Caudate_basal_ganglia.signifpairs.txt"
# [10] "Brain_Cerebellar_Hemisphere.signifpairs.txt"
# [11] "Brain_Cerebellum.signifpairs.txt"
# [12] "Brain_Cortex.signifpairs.txt"
# [13] "Brain_Frontal_Cortex_BA9.signifpairs.txt"
# [14] "Brain_Hippocampus.signifpairs.txt"
# [15] "Brain_Hypothalamus.signifpairs.txt"
# [16] "Brain_Nucleus_accumbens_basal_ganglia.signifpairs.txt"
# [17] "Brain_Putamen_basal_ganglia.signifpairs.txt"
# [18] "Brain_Spinal_cord_cervical_c-1.signifpairs.txt"
# [19] "Brain_Substantia_nigra.signifpairs.txt"
# [20] "Breast_Mammary_Tissue.signifpairs.txt"
# [21] "Cells_EBV-transformed_lymphocytes.signifpairs.txt"
# [22] "Cells_Transformed_fibroblasts.signifpairs.txt"
# [23] "Colon_Sigmoid.signifpairs.txt"
# [24] "Colon_Transverse.signifpairs.txt"
# [25] "Esophagus_Gastroesophageal_Junction.signifpairs.txt"
# [26] "Esophagus_Mucosa.signifpairs.txt"
# [27] "Esophagus_Muscularis.signifpairs.txt"
# [28] "Heart_Atrial_Appendage.signifpairs.txt"
# [29] "Heart_Left_Ventricle.signifpairs.txt"
# [30] "Liver.signifpairs.txt"
# [31] "Lung.signifpairs.txt"
# [32] "Minor_Salivary_Gland.signifpairs.txt"
# [33] "Muscle_Skeletal.signifpairs.txt"
# [34] "Nerve_Tibial.signifpairs.txt"
# [35] "Ovary.signifpairs.txt"
# [36] "Pancreas.signifpairs.txt"
# [37] "Pituitary.signifpairs.txt"
# [38] "Prostate.signifpairs.txt"
# [39] "Skin_Not_Sun_Exposed_Suprapubic.signifpairs.txt"
# [40] "Skin_Sun_Exposed_Lower_leg.signifpairs.txt"
# [41] "Small_Intestine_Terminal_Ileum.signifpairs.txt"
# [42] "Spleen.signifpairs.txt"
# [43] "Stomach.signifpairs.txt"
# [44] "Testis.signifpairs.txt"
# [45] "Thyroid.signifpairs.txt"
# [46] "Uterus.signifpairs.txt"
# [47] "Vagina.signifpairs.txt"
# [48] "Whole_Blood.signifpairs.txt"
tissues_of_interest <- GTEx_tissues[] # default is all tissues.
# alternatively the user can select specific tissues by
# providing the appropriate indices in the square brackets.
#------------------------------------------------------------------------------------------------------
## 4. EXECUTE ANNOTATION
source(file = file.path(base_dir, "ProGeM_functions.R")) # provided.
source(file = file.path(base_dir, "ProGeM_commands.R")) # provided.
#######################################################################################################