Publications by Mehak Chopra
gwsem - gXe
library(OpenMx) ## To take full advantage of multiple cores, use: ## mxOption(key='Number of Threads', value=parallel::detectCores()) #now ## Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx) install.packages("gwsem") ## Installing package into '/home/mchopra/R/x86_64-pc-linux-gnu-library/4.2' ## (as 'lib' is unspecifi...
262 sym R (7729 sym/32 pcs) 2 img
PGS analysis test 1
setwd("/home/mchopra/Documents/PhD-Year1/PRS/") library(RegParallel) ## Loading required package: doParallel ## Loading required package: foreach ## Loading required package: iterators ## Loading required package: parallel ## Loading required package: data.table ## Loading required package: stringr ## Loading required package: survival ## Loading r...
816 sym R (32208 sym/155 pcs) 3 img
Post_GWAS analysis
library(vcfR) ## ## ***** *** vcfR *** ***** ## This is vcfR 1.15.0 ## browseVignettes('vcfR') # Documentation ## citation('vcfR') # Citation ## ***** ***** ***** ***** library(ggplot2) #vcf_aao <- read.vcfR("/home/mchopra/Documents/PhD-Year1/GTEx/GTEx_aao.vcf") ##335 variant count #vcf_aao <- r...
990 sym R (48587 sym/298 pcs) 14 img
GTEx_file_sorting
library(biomaRt) library(immunedeconv) ## Loading required package: EPIC library(corrplot) ## corrplot 0.92 loaded library(forcats) library(stringr) library(here) ## here() starts at /home/mchopra/Documents/PhD-Year1/deconvolution library(dplyr) ## ## Attaching package: 'dplyr' ## The following object is masked from 'package:biomaRt': ## ## s...
1462 sym R (8387 sym/77 pcs) 2 img
lm_cell_proportions_with_age
library(ggplot2) library(dplyr) ## ## Attaching package: 'dplyr' ## The following objects are masked from 'package:stats': ## ## filter, lag ## The following objects are masked from 'package:base': ## ## intersect, setdiff, setequal, union library(tidyr) library(tibble) library(cowplot) library(metan) ## Registered S3 method overwritten ...
2084 sym R (18954 sym/367 pcs) 8 img
lm_cell_proportions_with_age
library(ggplot2) library(dplyr) ## ## Attaching package: 'dplyr' ## The following objects are masked from 'package:stats': ## ## filter, lag ## The following objects are masked from 'package:base': ## ## intersect, setdiff, setequal, union library(tidyr) library(tibble) library(cowplot) library(metan) ## Registered S3 method overwritten ...
2087 sym R (134793 sym/370 pcs) 8 img
Correlation Test
library("metan") ## Registered S3 method overwritten by 'GGally': ## method from ## +.gg ggplot2 ## |=========================================================| ## | Multi-Environment Trial Analysis (metan) v1.18.0 | ## | Author: Tiago Olivoto | ## | Type 'citation('metan')' to know how to cite metan...
142 sym R (4875 sym/31 pcs) 3 img
Inverse Normal Distribution
file <- read.csv("/home/mchopra/Documents/PhD-Year1/results_imaging/pheno_aao.csv", h = T) file[1:1, 1:3] ## X AAo_distensibility DAo_distensibility ## 1 1000095 1.666458 2.272647 #the following is after removal of 2 outlier phenotype (1145696 - 140.65 and 1869683 - 637.99) summary(file$AAo_distensibility) ## Min. 1st...
729 sym R (4783 sym/47 pcs) 6 img
Deconvolution - cellular composition
library(ggplot2) library(dplyr) ## ## Attaching package: 'dplyr' ## The following objects are masked from 'package:stats': ## ## filter, lag ## The following objects are masked from 'package:base': ## ## intersect, setdiff, setequal, union library(tidyr) library(tibble) library(cowplot) library(metan) ## Registered S3 method overwritten ...
315 sym R (24282 sym/54 pcs) 7 img