Fan Wang wangfan860
wangfan860
/ predicted_vs_real_expression.py
Last active
November 22, 2019 16:48
For comparison between TCGA-BRCA real expression with predicted gene expression. Raw Pearson is low even in normal tissue samples. Integrate quantile normalization and inverse quantile normalization to process the real expression in the last part
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| from gtfparse import read_gtf | |
| import pandas as pd | |
| import seaborn as sns | |
| import matplotlib.pyplot as plt | |
| import numpy as np | |
| import gzip | |
| import subprocess | |
| import scipy.stats as stats | |
| import argparse | |
| import os |
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| if (!require("BiocManager")) | |
| install.packages("BiocManager") | |
| BiocManager::install("maftools") | |
| ##download rngtools from https://cran.r-project.org/src/contrib/Archive/rngtools/ | |
| install.packages("~/Desktop/nature_commu/rngtools_1.3.1.tar.gz", repos = NULL, type = "source") | |
| library(maftools) | |
| uvm = read.maf(maf = '.maf') | |
| skcm = read.maf(maf = '.maf') | |
| # download CanFam3.1 from ftp://ftp.ensembl.org/pub/release-96/gtf/canis_familiaris/ |
wangfan860
/ oncoprint_plot.r
Created
May 7, 2019 17:03
simple function to plot oncoprint for few genes
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| # This function sorts the matrix for better visualization of mutual exclusivity across genes | |
| memoSort <- function(M) { | |
| geneOrder <- sort(rowSums(M), decreasing=TRUE, index.return=TRUE)$ix; | |
| scoreCol <- function(x) { | |
| score <- 0; | |
| for(i in 1:length(x)) { | |
| if(x[i]) { | |
| score <- score + 2^(length(x)-i); | |
| } | |
| } |
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| #be sure to have scikit-allel, pandas, glob intalled | |
| import allel | |
| import pandas as pd | |
| import glob | |
| #change this line to match the path for vcf.gz files | |
| all_files = glob.glob("*.vcf.gz") | |
| #very first vcf for merging | |
| file1 = allel.read_vcf(all_files[0]) |