Methylation QTL (mQTL) Resources on FunGen-AD Resources

Knight ADRC brain methylation QTL

Mon, 01 Jan 0001 00:00:00 +0000

Knight ADRC brain methylation QTL#

Contact#

Alexandre Pelletier

Links to QTL analysis notebooks#

See notebooks in:

https://github.com/cumc/xqtl-analysis/tree/main/analysis/Wang_Columbia/KnightADRC/mQTL

The notebooks in this folder contain the commands and data wrangling codes for analysis of the methylation data in KnightADRC. (data wrangling exist because not all data are processed using the xqtl-pipeline from the beginning and need to be reformatted to fit one intermediate step of the pipeline).

Association data preprocessing#

KnightADRC_mQTL_Preprocessing_Analysis.ipynb shows the commands used for genotype/phenotype/covariate processing and preparation steps.

Association scan using TensorQTL and summary statistics standardization#

TensorQTL.ipynb provides the pipeline to generate TensorQTL cis association results for all QTLs.
Knight_mQTL_commands provides information about the input files for TensorQTL cis association in the base_params variable in [generate_command_1].

Path(s) to cis-QTL association testing#

output of TensorQTL.ipynb

MSBB brain methylation QTL

Mon, 01 Jan 0001 00:00:00 +0000

MSBB brain methylation QTL#

Contact#

Alexandre Pelletier

Links to QTL analysis notebooks#

See notebooks in:

https://github.com/cumc/xqtl-analysis/tree/main/analysis/Wang_Columbia/MSBB/mQTL

The notebooks in this folder contain the commands and data wrangling codes for analysis of the expression data in MSBB. (data wrangling exist because not all data are processed using the xqtl-pipeline from the beginning and need to be reformatted to fit one intermediate step of the pipeline).

Association data preprocessing#

Genotype_preprocessing provides steps for PCA analysis for genotype data. Phenotype_preprocessing shows the commands used for the phenotype data processing and preparation steps. Covariates_preprocessing shows the commands used for the covariate data processing and preparation steps. details please see https://github.com/cumc/xqtl-analysis/tree/main/analysis/TCW_BU/MSBB/mqtl/scripts

ROSMAP DLPFC methylation QTL

Mon, 01 Jan 0001 00:00:00 +0000

ROSMAP DLPFC methylation QTL#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC methylation data-set.

Please refer to this document for an overview of the ROSMAP project.

Contact#

Alexandre Pelletier

Links to QTL analysis notebooks#

See notebooks in:

https://github.com/cumc/xqtl-analysis/tree/main/analysis/TCW_BU/ROSMAP/mqtl