Add TensorQTL support to eQTL mapping function and update README#14
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charliewang123 wants to merge 49 commits into
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Add TensorQTL support to eQTL mapping function and update README#14charliewang123 wants to merge 49 commits into
charliewang123 wants to merge 49 commits into
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- eQTL mapping parameters are provided as options in the function instead of hard coded (e.g. model, cis distance, p-value threshold etc) - output_file_name_cis = paste0(out_dir, context, "_", shared_specific, ".all_pairs.txt"); -> output_file_name_cis needs to be a parameter in the function - output_file_name_tra = tempfile(); -> output_file_name_tra needs to be a parameter in the function - genepos = read.table(file = …)[,1:4]; -> Instead of column numbers you need to ask for column names - snpspos = read.table(file = …)[,1:3]; -> Instead of column numbers you need to ask for column names - tensorQTL output needs to match MatrixEQTL output - p-values in tensorQTL output need to be ordered in ascending order (0,1)
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eQTL_mapping_step()using reticulate