Reorder Matrix

Results

Original instructions in the code kept, see the comments.

Stored on server: /space/chen-syn01/1/data/cinliu/data/2020archive/reorder_cor

1st edit

8.reorder_cor_mat_edit1.R

rm(list=ls())

library(graph4lg)

library(reshape2)

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dir <- "/space/chen-syn01/1/data/chen/gwas_gclust/genesis/ABCD/"

pheno_dir <- "/space/chen-syn01/1/data/cmakowski/ABCD/GCLUST/GWAS/Science_revisions/"

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load(paste0(dir,"GRM_adj.RData"))

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IID <- read.table(paste0(pheno_dir,"/genotype_QCed/ABCD_ALL.fam"),sep=" ",h=F)

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#reorder

matrix <- as.matrix(GRM_adj) #before reordering

order1 <- IID$V1

reordered_GRM_adj <- reorder_mat(mat = matrix, order = order1) # using graph4lg package

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#convert the correlation matrix format into a table format:

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####SAVING THE ENTRIE MATRIX TO DATATABLE ####

#data <- melt(mat, value.name = "grm", varnames=c('ID1', 'ID2')) #reshape2 package

#write.csv(data,"all_melt.csv", row.names = FALSE) #save a copy of all

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#generate one table from upper triangular and one from lower triangular part.

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###LOWER ONLY ####

lower<-reordered_GRM_adj

lower[upper.tri(reordered_GRM_adj, diag=TRUE)] <- NA

lower_melt <- melt(lower)

lower_melt <- na.omit(lower_melt)

colnames(lower_melt) <- c('ID1', 'ID2', "grm")

write.csv(lower_melt,"lower_table_format.csv", row.names = FALSE)

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###UPPER ONLY ####

upper<-reordered_GRM_adj

upper[lower.tri(reordered_GRM_adj)] <- NA

upper_melt <- melt(upper)

upper_melt <- na.omit(upper_melt)

colnames(upper_melt) <- c('ID1', 'ID2', "grm")

write.csv(upper_melt,"upper_table_format.csv", row.names = FALSE)

Hello Nini, we need your help on a task. please see the same file with the instruction from Line 30

"/space/chen-syn01/1/data/chen/gwas_gclust/genesis/ABCD/8.reorder_cor_mat.R"

2nd edit

8.reorder_cor_mat_edit2.R

rm(list=ls())

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dir <- "/space/chen-syn01/1/data/chen/gwas_gclust/genesis/ABCD/"

pheno_dir <- "/space/chen-syn01/1/data/cmakowski/ABCD/GCLUST/GWAS/Science_revisions/"

​

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#use the subject list FILE1 below and find their grm values in the matrix above, GRM_adj

load(paste0(dir,"GRM_adj.RData"))

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#FILE1: /space/chen-syn01/1/data/cmakowski/ABCD/ABCD_zygozygosity.2020_04_19.check.csv # need to read this file into R

FILE1 <- read.csv("~/Desktop/2020lab/plots/CH/ABCD_zygozygosity.2020_04_19.check.csv") #UPDATE

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df <- FILE1[,1:2]

df$grm <- NA

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#loop will put NA in location where no matches are found

for (i in 1:nrow(df)) {

x <- paste0(GRM_adj[colnames(GRM_adj) == FILE1$IID1[i] , rownames(GRM_adj) == FILE1$IID2[i]])

if (identical(x, character(0)) == TRUE) {

df$grm[i] <- NA

}else{

df$grm[i] <- x

}

}

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write.csv(df,"output.csv", row.names = FALSE)