Comments (2)
Hi Alvaro,
Thank you so much for such a quick response. For the case that I only have eQTL summary statistics from 1 tissue, what is the best way to generate the model? (I assume that MASHR does not work for single tissue here).
Thanks in advance,
Yingbo
from metaxcan.
Hi Tingbo,
Indeed that repository provides one way to generate S-PrediXcan (and PrediXcan) models from QTL summary statistics.
If you have multiple tissues, you can instead ran MASHR on the summary statistics and use the corrected effect sizes to build linear models for experesion.
Best,
Alvaro
from metaxcan.
Related Issues (20)
- Question to SMulTiXcans pvalue HOT 2
- Create predictcan model from eQTL sum statistics
- MLE_did_not_converge
- Variants and genes in the mashr_Brain_Spinal_cord_cervical_c-1.db HOT 1
- The variant_id in GWAS Summary data can be CHR:POS:REF:ALT instead of rsid HOT 4
- Predict.py with imputation data HOT 4
- Error in installing MetaXcan and creating the environment in the LISA SURFSARA system HOT 1
- Problem creating covariance for s-mutlixcan HOT 1
- Problems with input data HOT 3
- How does PrediXcan with mashr model deal with missing genotype?
- Good meta-analysis method after predixcan HOT 1
- Only running 3 genes when using files I just pulled from PredictDB
- Very few SNPs used when using Michigan imputed data
- Too slow for calculating the expression level Tg
- S-MultiXcan results files - not all genes from individual tissues present HOT 2
- S-MultiXcan: extracting exact z-scores used to compute p-values (for p < e-324) HOT 3
- heritability estimates of gtex-v8 genes
- Requesting help:about QTL_to_PredictDB: AttributeError: 'NoneType' object has no attribute 'endswith'
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