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07a-htmcp_load_bulk.R
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07a-htmcp_load_bulk.R
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################################################################################
################################################################################
################################################################################
################################################################################
########################## HTMCP DATA / METADATA SETUP ########################
#################################### SETUP #####################################
library(tidyverse)
library(readxl)
library(GenomicDataCommons)
library(TCGAbiolinks)
library(dplyr)
library(rtracklayer)
library(data.table)
library(scopetools)
library(tximport)
################################### LOAD DATA ##################################
load("r_outputs/01-refs.Rdata")
load("r_outputs/01-all_lymphoma_counts.Rdata")
load("r_outputs/01-DLBCL_counts.Rdata")
############################ LOAD GENE ANNOTATIONS #############################
ttg <- read.table('refs/ttg.tsv',
sep = '\t',
header = T,
stringsAsFactors = F
)
gsym <- read.table('refs/gsym.tsv',
sep = '\t',
header = T,
stringsAsFactors = F
)
row.names(gsym) <- gsym$GENEID
gsym$display <- gene_table$display[match(gsym$SYM, gene_table$gene_name)]
gsym$display <- ifelse(is.na(gsym$display), gsym$SYM, gsym$display)
gsym[duplicated(gsym$display), 'display'] <-
paste(gsym[duplicated(gsym$display), 'display'],
gsym[duplicated(gsym$display), 'GENEID'], sep='|')
HTMCP_metadata <- read.csv('metadata/HTMCP/samples_hiv_dlbcl.csv', stringsAsFactors = F) %>%
dplyr::select(sample_id=BioSample, primary_site=body_site) %>%
dplyr::mutate(
primary_site=factor(recode(primary_site, `lymph node`='LN', `blood`='BL'),
levels=c('LN','BL')),
HIV=factor("positive", levels=c('negative', 'positive'))
)
row.names(HTMCP_metadata) <- HTMCP_metadata$sample_id
################################## LOAD HTMCP ##################################
files <- file.path('results/HTMCP/kallisto_alignment', rownames(HTMCP_metadata),
paste0(rownames(HTMCP_metadata), ".", 'kallisto.abundance.tsv'))
names(files) <- rownames(HTMCP_metadata)
txi <- tximport(files, type = "kallisto", tx2gene=ttg)
hiv.pos.DLBCL.counts.tx <- as.data.frame(txi$counts)
row.names(hiv.pos.DLBCL.counts.tx) <- gsym[rownames(hiv.pos.DLBCL.counts.tx),]$display
################################ LOAD TELESCOPE ###############################
#--- Load Telescope counts
files <- file.path('results/HTMCP/telescope', rownames(HTMCP_metadata),
paste0(rownames(HTMCP_metadata), "-", 'telescope_report.tsv'))
names(files) <- rownames(HTMCP_metadata)
cts <- lapply(1:length(files),
function(i) {
tmp <- read.table(files[i],
sep='\t', header=T, stringsAsFactors=F)
ret <- data.frame(
transcript=retro.annot$locus,
stringsAsFactors = F
) %>%
left_join(tmp, by='transcript') %>%
dplyr::select(gene_id=transcript, count=final_count)
ret[is.na(ret)] <- 0
stopifnot(all(ret$gene_id == retro.annot$locus))
ret$gene_id <- NULL
names(ret) <- c(names(files)[i])
ret
}) %>% bind_cols
row.names(cts) <- retro.annot$locus
rxi <- list(counts=cts)
################################ GENE IDs IN TXI ###############################
row.names(DLBCL.counts.tx) <- gene_table[rownames(DLBCL.counts.tx),]$display
row.names(all.counts.tx) <- gene_table[rownames(all.counts.tx),]$display
tx <- list(hiv.pos.DLBCL.counts.tx, DLBCL.counts.tx, all.counts.tx)
common_names = Reduce(intersect, lapply(tx, row.names))
DLBCL.counts.tx <- DLBCL.counts.tx[row.names(DLBCL.counts.tx) %in% common_names,]
all.counts.tx <- all.counts.tx[row.names(all.counts.tx) %in% common_names,]
hiv.pos.DLBCL.counts.tx <- hiv.pos.DLBCL.counts.tx[row.names(hiv.pos.DLBCL.counts.tx) %in% common_names,]
# Reorder
reorder_idx_counts.tx <- match(common_names, rownames(hiv.pos.DLBCL.counts.tx))
hiv.pos.DLBCL.counts.tx <- hiv.pos.DLBCL.counts.tx[reorder_idx_counts.tx,]
reorder_idx_counts.tx <- match(common_names, rownames(DLBCL.counts.tx))
DLBCL.counts.tx <- DLBCL.counts.tx[reorder_idx_counts.tx,]
reorder_idx_counts.tx <- match(common_names, rownames(all.counts.tx))
all.counts.tx <- all.counts.tx[reorder_idx_counts.tx,]
stopifnot(all(rownames(all.counts.tx) == rownames(hiv.pos.DLBCL.counts.tx)))
stopifnot(all(rownames(DLBCL.counts.tx) == rownames(hiv.pos.DLBCL.counts.tx)))
################################ COMBINE SAMPLES ###############################
# all counts
stopifnot(all(rownames(cts) == rownames(all.counts.rtx)))
all.counts.hiv.rtx <- cbind(cts, all.counts.rtx)
all.counts.hiv.tx <- cbind(hiv.pos.DLBCL.counts.tx, all.counts.tx)
all.counts.hiv.comb <- rbind(all.counts.hiv.tx, all.counts.hiv.rtx)
# dlbcl counts
stopifnot(all(rownames(cts) == rownames(DLBCL.counts.rtx)))
DLBCL.hiv.counts.rtx <- cbind(cts, DLBCL.counts.rtx)
DLBCL.hiv.counts.tx <- cbind(hiv.pos.DLBCL.counts.tx, DLBCL.counts.tx)
DLBCL.hiv.counts.comb <- rbind(DLBCL.hiv.counts.tx, DLBCL.hiv.counts.rtx)
############################# SUBSET HERVs and L1s #############################
# all counts
all.counts.hiv.herv <- all.counts.hiv.rtx[retro.hg38.v1$te_class == 'LTR',]
all.counts.hiv.l1 <- all.counts.hiv.rtx[retro.hg38.v1$te_class == 'LINE',]
# dlbcl counts
DLBCL.counts.hiv.herv <- DLBCL.hiv.counts.rtx[retro.hg38.v1$te_class == 'LTR',]
DLBCL.counts.hiv.l1 <- DLBCL.hiv.counts.rtx[retro.hg38.v1$te_class == 'LINE',]
################################ COMBINE METADATA ##############################
# all counts
HTMCP_metadata_formatted <- HTMCP_metadata
HTMCP_metadata_formatted$cancer_type <- "DLBCL"
HTMCP_metadata_formatted$subtype <- "HIV-positive"
all_metadata_hiv <-
rbind(
subset(HTMCP_metadata_formatted, select = c("cancer_type", "subtype")),
all_metadata
)
# dlbcl
DLBCL_metadata_hiv <- dplyr::bind_rows(
subset(HTMCP_metadata_formatted, select = c("cancer_type", "subtype")),
DLBCL_metadata)
##########################@###### SANITY CHECK ##########@######################
stopifnot(all(names(DLBCL.hiv.counts.rtx) == rownames(DLBCL_metadata_hiv)))
stopifnot(all(names(DLBCL.hiv.counts.comb) == rownames(DLBCL_metadata_hiv)))
stopifnot(all(names(all.counts.hiv.rtx) == rownames(all_metadata_hiv)))
stopifnot(all(names(all.counts.hiv.comb) == rownames(all_metadata_hiv)))
################################## SAVE FILES ##################################
save(all.counts.hiv.tx, all.counts.hiv.rtx, all.counts.hiv.comb,
all.counts.hiv.herv, all.counts.hiv.l1, all_metadata_hiv,
file="r_outputs/07-htmcp_all_lymphoma_counts.Rdata")
save(DLBCL.hiv.counts.tx, DLBCL.hiv.counts.rtx, DLBCL.hiv.counts.comb,
DLBCL.counts.hiv.herv, DLBCL.counts.hiv.l1, DLBCL_metadata_hiv,
file="r_outputs/07-htmcp_dlbcl_counts.Rdata")