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condense_hsq.R
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library('SummarizedExperiment')
library('sessioninfo')
files <- c(
'DLPFC' = '/dcl01/lieber/ajaffe/lab/brainseq_phase2/twas/DLPFC/gene/heritability/hsq_info.Rdata',
'HIPPO' = '/dcl01/lieber/ajaffe/lab/brainseq_phase2/twas/HIPPO/gene/heritability/hsq_info.Rdata'
)
# rse_files <- c(
# 'DLPFC' = '/dcl01/lieber/ajaffe/lab/brainseq_phase2/twas/DLPFC/gene/subsetted_rse.Rdata',
# 'HIPPO' = '/dcl01/lieber/ajaffe/lab/brainseq_phase2/twas/HIPPO/gene/subsetted_rse.Rdata'
# )
#
# rse <- lapply(rse_files, function(f) {
# load(f, verbose = TRUE)
# return(rse)
# })
## Genes are the same Same for both regions
load('/dcl01/lieber/ajaffe/lab/brainseq_phase2/twas/DLPFC/gene/subsetted_rse.Rdata', verbose = TRUE)
genes <- names(rowRanges(rse))
hsq <- lapply(files, function(f) {
load(f, verbose = TRUE)
missing <- genes[!genes %in% hsq_info$ID]
if(length(missing) > 0) {
add <- data.frame(
HSQ = NA,
ID = missing,
CHR = gsub('chr', '', as.character(seqnames(rowRanges(rse)[missing]))),
P0 = start(rowRanges(rse)[missing]),
P1 = end(rowRanges(rse)[missing]),
geneID = missing,
hsq = NA,
hsq.se = NA,
hsq.pv = NA,
region = hsq_info$region[1],
feature = hsq_info$feature[1],
failFilter = NA,
stringsAsFactors = FALSE
)
hsq_info <- rbind(hsq_info, add)
}
hsq_info <- hsq_info[match(genes, hsq_info$ID), ]
rownames(hsq_info) <- NULL
return(hsq_info)
})
names(hsq) <- names(files)
## Genes that didn't converge
sapply(hsq, function(x) { sum(is.na(x$HSQ))})
# DLPFC HIPPO
# 568 600
## Genes that didn't converge across regions
addmargins(table(
'DLPFC' = is.na(hsq[['DLPFC']]$HSQ),
'HIPPO' = is.na(hsq[['HIPPO']]$HSQ)
))
# HIPPO
# DLPFC FALSE TRUE Sum
# FALSE 22284 550 22834
# TRUE 518 50 568
# Sum 22802 600 23402
## Number of genes that pass the heritability filters
sapply(hsq, function(x) { table(!x$failFilter, useNA = 'ifany')})
# DLPFC HIPPO
# FALSE 15147 16934
# TRUE 7687 5868
# <NA> 568 600
## genes passing filters across regions
addmargins(table(
'DLPFC' = !hsq[['DLPFC']]$failFilter,
'HIPPO' = !hsq[['HIPPO']]$failFilter,
useNA = 'ifany'
))
# HIPPO
# DLPFC FALSE TRUE <NA> Sum
# FALSE 13622 1020 505 15147
# TRUE 2806 4836 45 7687
# <NA> 506 12 50 568
# Sum 16934 5868 600 23402
## Explore a bit how the heritability across regions looks
plot(x = hsq[['DLPFC']]$hsq, y = hsq[['HIPPO']]$hsq, xlab = 'DLPFC', ylab = 'HIPPO')
save(hsq, file = 'rda/hsq_genes.Rdata')
## Resume
load('rda/hsq_genes.Rdata', verbose = TRUE)
add.alpha <- function(col, alpha=1){
if(missing(col))
stop("Please provide a vector of colours.")
apply(sapply(col, col2rgb)/255, 2,
function(x)
rgb(x[1], x[2], x[3], alpha=alpha))
}
pdf('pdf/heritability_DLPFC_HIPPO_gene.pdf', useDingbats = FALSE)
plot(
x = (hsq[['DLPFC']]$hsq + hsq[['HIPPO']]$hsq) / 2,
y = hsq[['DLPFC']]$hsq - hsq[['HIPPO']]$hsq,
xlab = '(DLPFC + HIPPO) / 2',
ylab = 'DLPFC - HIPPO',
pch = 16,
col = ifelse(
!(hsq[['DLPFC']]$failFilter | hsq[['HIPPO']]$failFilter),
add.alpha('magenta', 1/5),
ifelse(
hsq[['DLPFC']]$hsq < 0 | hsq[['HIPPO']]$hsq < 0,
add.alpha('royalblue4', 1/5),
add.alpha('black', 1/5)
)
),
main = 'Heritability (cis +- 500kb)',
cex.lab = 1.4,
cex.axis = 1.4,
cex.main = 1.5
)
abline(h = 0, col = 'red', lwd = 1.2)
legend('bottomright',
legend = c(
'<0 in 1 region',
'Fails filter in 1 region',
'Passes filters in both regions'
),
col = c('royalblue4', 'black', 'magenta'), lwd = 2
)
plot(
x = hsq[['HIPPO']]$hsq,
y = hsq[['DLPFC']]$hsq,
xlab = 'HIPPO',
ylab = 'DLPFC',
pch = 16,
col = ifelse(
!(hsq[['DLPFC']]$failFilter | hsq[['HIPPO']]$failFilter),
add.alpha('magenta', 1/5),
ifelse(
hsq[['DLPFC']]$hsq < 0 | hsq[['HIPPO']]$hsq < 0,
add.alpha('royalblue4', 1/5),
add.alpha('black', 1/5)
)
),
main = 'Heritability (cis +- 500kb)',
cex.lab = 1.4,
cex.axis = 1.4,
cex.main = 1.5
)
abline(a = 0, b = 1, col = 'red', lwd = 1.2)
legend('bottomright',
legend = c(
'<0 in 1 region',
'Fails filter in 1 region',
'Passes filters in both regions'
),
col = c('royalblue4', 'black', 'magenta'), lwd = 2
)
dev.off()
## Reproducibility information
print('Reproducibility information:')
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 3.5.3 Patched (2019-03-11 r76311)
# os Red Hat Enterprise Linux Server release 6.9 (Santiago)
# system x86_64, linux-gnu
# ui X11
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz US/Eastern
# date 2019-05-01
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
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# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 3.5.1)
# SummarizedExperiment * 1.12.0 2018-10-30 [1] Bioconductor
# tibble 2.1.1 2019-03-16 [1] CRAN (R 3.5.3)
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#
# [1] /users/lcollado/R/x86_64-pc-linux-gnu-library/3.5.x
# [2] /jhpce/shared/jhpce/core/conda/miniconda-3/envs/svnR-3.5.x/R/3.5.x/lib64/R/site-library
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