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andreyshabalin / MatrixEQTL

Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
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calculation only cis-eQTL #22

Closed Asppagh closed 1 year ago

Asppagh commented 1 year ago

Is there any option to calculate cis-eQTL ? currently is does both cis and trans at the same time, but in many case we need to do only one of them. Thanks!

andreyshabalin commented 1 year ago

Yes, set distant eQTL p-value threshold to 0.

andreyshabalin commented 1 year ago

Per http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/html/Matrix_eQTL_main.html

Set pvOutputThreshold = 0 and pvOutputThreshold.cis > 0 to perform eQTL analysis for local gene-SNP pairs only. Local associations significant at pvOutputThreshold.cis level will be recorded in output_file_name.cis and in the returned object.