2021-04-07-optim-multi-scalar-pi-gama
123456# compact_data = readRDS("/storage11_7T/fuy/TADA-A/annotation/spliceai/2021-03-15_spliceai_DS_AG_6788SNV_sf_uni_prior_compact.rds")com ...
2021-04-07-PPI-annotation
PPI-MPC212library(tadaA)setwd("/storage11_7T/fuy/TADA-A/annotation")
12345678910111213141516171819202122232425262728293031323334system.tim ...
2021-03-26-multi-annota-RR-optim-test
12345678910111213141516# compact_data = readRDS("/storage11_7T/fuy/TADA-A/annotation/spliceai/2021-03-15_spliceai_DS_AG_6788SNV_sf_uni_prior_comp ...
2021-03-29-tadaA-report
目前进展1） 用Rcpp改进算法，单独一个估参约，速度为之前的1/2，多组联合估参速度加快较明显，5组7h vs 1.2h
2） 完成simulation，确认EM结果
如果用posterior更新pi，则得到的gama != simulated gama
若只更新gama，则得到的avera ...
2021-03-25-optim-multi-scalar-pi-gama
123456# compact_data = readRDS("/storage11_7T/fuy/TADA-A/annotation/spliceai/2021-03-15_spliceai_DS_AG_6788SNV_sf_uni_prior_compact.rds")com ...
2021-03-25-optim-update-posterior-pi
2021-03-25-optim-update-posterior-pi
/*!
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/*!
* Bootstrap v3.3.7 (http://getbootstrap.com)
* Copyright 2011 ...
2021-03-22-simulation
2021-03-22-simulation
/*!
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* Twitter Bootstrap
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/*!
* Bootstrap v3.3.7 (http://getbootstrap.com)
* Copyright 2011-2016 Twitter, ...
2021-03-18-tadaA-report
Notes:
Data structure array
EM rectify
Optim
Annotation 占总数的比值，是否过于conserved, overlap heatmap
Estimation of indel rateSNV_rate: 2N * summation over ...
2021-01-13-tadaA-report
DNM data we used in the analysis1readRDS("/storage11_7T/fuy/TADA-A/cell_WES/DNM/DNM_descrip.rds")
A data.frame: 2 × 3
n_samplen_DNMd ...
201126-tadaA-report
overview of the dataset in the paper :
15,789 de novo variants
12166 in 6430 affected individuals.
5951 SNVs in our autosomal coding windows.
3623 ...