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.Rhistory
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library(devtools)
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
devtools::check()
q()
n
library(devtools)
check()
check()
check()
source("~/git/dryclean/R/dryclean.R")
source("~/git/dryclean/R/dryclean.R")
normal.table.path = "/gpfs/commons/home/adeshpande/normal.table.rds"
num.cores = 5
samp.final[, sample][1]
nm = samp.final[, sample][1]
this.cov
field = "reads.corrected"
reads
summary(reads)
this.cov
this.cov %Q% (seqnames == "22")
this.cov
summary(this.cov)
summary(this.cov)
summary(this.cov)
summary(reads)
summary(reads)
summary(reads)
summary(reads)
mat.n[[1]]
is.human = TRUE
any(is.infinite(mat.bind))
dim(mat.bind)
mat.bind[,1]
asd = rowSums(mat.bind)
asd
gc()
mat.bind.t
samp.final[87]
nm = "PM763-Z3-1"
this.cov
this.cov
summary(this.cov)
this.cov[signal >0]
this.cov
reads
this.cov
this.cov
this.cov
this.cov
summary(this.cov)
reads
min.cov
readds
reads
reads[signal > 0 & !is.infinite(signal)]
any(is.infinite(reads))
reads = data.table(NULL)
reads
is.null(reads)
samp.fianl
samp.fina;
samp.final
samp.final
samp.final[86:88]
nm
samp.final = samp.final[86:88]
samp.final
mat.n
mat.n
c
gc()
mat.n[[2]]
gc()
gc()
dim(mat.n[[1]])
dim(mat.n[[2]])
dim(mat.n[[2]])
dim(mat.n[[1]])
mat.bind.t
summary(mat.bind.t)
source("~/git/dryclean/R/dryclean.R")
source("~/git/dryclean/R/dryclean.R")
detergent2 = prepare_detergent(normal.table.path = "/gpfs/commons/home/adeshpande/normal.table.rds", path.to.save = "/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/tmp_122_samp/", num.cores = 5, use.all = TRUE)
ipm.case
all.chr = c(as.character(1:22), "X", "Y")
all.chr
Sys.setenv(DEFAULT_BSGENOME = "BSgenome.Hsapiens.UCSC.hg19::Hsapiens")
all.chr = c(as.character(1:22), "X")
source("~/git/dryclean/R/dryclean.R")
source("~/git/dryclean/R/dryclean.R")
detergent2 = prepare_detergent(normal.table.path = "/gpfs/commons/home/adeshpande/normal.table.rds", path.to.save = "/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/tmp_122_samp/", num.cores = 5, use.all = TRUE)
nm
normal.table
nm = "23430-B52-T"
samp.final
nm = "PM753-Z2-1"
this.cov
reads
reads
source("~/git/dryclean/R/dryclean.R")
detergent2 = prepare_detergent(normal.table.path = "/gpfs/commons/home/adeshpande/normal.table.rds", path.to.save = "/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/tmp_122_samp/", num.cores = 5, use.all = TRUE)
saveRDS(detergent2, "/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/tmp_122_samp/detergent_general.rds")
check()
check()
skittols::mem()
skitools::mem()
getwd()
check()
prepare_cov
prepare_detergent
detergent2 = prepare_detergent(normal.table.path = "/gpfs/commons/home/adeshpande/normal.table.rds", path.to.save = "/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/tmp_122_samp/", num.cores = 5, use.all = TRUE)
kill.zombies()
gc()
source("~/git/dryclean/R/dryclean.R")
prepare_detergent
detergent2 = prepare_detergent(normal.table.path = "/gpfs/commons/home/adeshpande/normal.table.rds", path.to.save = "/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/tmp_122_samp/", num.cores = 5, use.all = TRUE)
gc()
normal.table
source("~/git/dryclean/R/dryclean.R")
asd = readRDS("/gpfs/commons/home/adeshpande/normal.table.rds")
asd
saveRDS(asd[1:5], "/gpfs/commons/home/adeshpande/normal.table.5.rds")
asd readRDS("/gpfs/commons/home/adeshpande/normal.table.5.rds")
asd = readRDS("/gpfs/commons/home/adeshpande/normal.table.5.rds")
asd
detergent2 = prepare_detergent(normal.table.path = "/gpfs/commons/home/adeshpande/normal.table.5.rds", path.to.save = "/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/tmp_122_samp/", num.cores = 5, use.all = TRUE)
source("~/git/dryclean/R/rrpca.mod.R")
source("~/git/dryclean/R/rrpca.mod2.R")
detergent2 = prepare_detergent(normal.table.path = "/gpfs/commons/home/adeshpande/normal.table.5.rds", path.to.save = "/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/tmp_122_samp/", num.cores = 5, use.all = TRUE)
sessionInfo()
pairs.ipm.sub
asd = readRDS("/gpfs/commons/home/adeshpande/normal.table.rds")
asd
pon = readRDS("/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/detergent.rds")
dim(pon$L)
pon = readRDS("/gpfs/commons/groups/imielinski_lab/data/dryclean/IPM_WGS_1kb_PON/Xchr_processed/detergent.rds")
dim(pon$L)
ipm.dr
lls()
ls()
library(MASS)
asd
all.chr = c(as.character(1:22), "X")
library(devtools)
check()
check()
check()
ls()
q()
n