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Arch4_Installation_GEO_retrieval_title_parsing.R
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Arch4_Installation_GEO_retrieval_title_parsing.R
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# R script to download selected samples
# Copy code and run on a local machine to initiate download
#https://docs.google.com/document/d/1jm1sJtHgJkSV7hEjMC_VK7l7gzshMQzr4T7NdgY9rGE/edit#heading=h.skn982pchl79
#https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930834/
# Check for dependencies and install if missing
packages <- c("rhdf5","pkgconfig")
if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
BiocManager::install("rhdf5")
}
#make ~/.R/Makevars and add the following (remove # in the beginning of each line)
# LDFLAGS= -L/usr/local/clang4/lib
# FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
# CC=/usr/local/clang4/bin/clang
# CXX=/usr/local/gfortran/bin/g++
# CXX1X=/usr/local/gfortran/bin/g++
# CXX98=/usr/local/gfortran/bin/g++
# CXX11=/usr/local/gfortran/bin/g++
# CXX14=/usr/local/gfortran/bin/g++
# CXX17=/usr/local/gfortran/bin/g++
#
# LLVM_LOC = /usr/local/opt/llvm
# CC=/usr/local/gfortran/bin/gcc -fopenmp
# CXX=/usr/local/gfortran/bin/g++ -fopenmp
# # -O3 should be faster than -O2 (default) level optimisation ..
# CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
# CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
# LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
# CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
#add this path to your mac: /usr/local/gfortran/bin
#If you have data.table error: ‘datatable.so’ not found
#https://github.com/Rdatatable/data.table/wiki/Installation#openmp-enabled-compiler-for-mac
# sample size
# platform: not array
# year
# organism
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
if (!requireNamespace("GEOquery", quietly = TRUE))
install.packages("GEOquery")
library("rhdf5")
library("tools")
library("GEOquery")
setwd("~/Dropbox (Gladstone)/Pathway-Project/human_matrix_download.h5")
destination_file = "human_matrix_download.h5"
data <- getGEO("GSE67492")
data$GSE67492_series_matrix.txt.gz@experimentData@title
data$GSE67492_series_matrix.txt.gz@experimentData@abstract
gse = h5read(destination_file, "meta/Sample_series_id")
head(gse)
length(gse)
238522
length(unique(gse))
7909
unique_gse=unique(gse)
###gse issue example: "GSE27452Xx-xXGSE32303"
##removing
library(stringr)
str_count(unique_gse[3],"GSE")
GSE_counts=apply(unique_gse,1,function(x) str_count(x,"GSE"))
max(GSE_counts)
3
length(which(GSE_counts>1))
1607
unique_gse=unique_gse[-which(GSE_counts>1)]
dieases=c("Renal cell carcinoma","Alzheimer’s disease","Alzheimer","Thyroid cancer","Dilated cardiomyopathy",
"Colorectal cancer","Prostate cancer","Huntington’s disease","Huntington","Acute Myeloid Leukemia",
"Pancreatic cancer","Non-small cell lung cancer","Glioma","Parkinson’s disease","Parkinson",
"Type II diabetes mellitus","Type 2 diabetes mellitus","Chronic Myeloid Leukemia","Endometrial cancer")
match_gse_disease<-function(gse_id){
print(gse_id)
tryCatch({
data <- getGEO(gse_id)
}, error = function(err) {
return(-1)
}) # END tryCatch
title=data[[1]]@experimentData@title
abstract=data[[1]]@experimentData@abstract
matched_disease_title=apply(as.matrix(dieases),1,function(x) grep(x,title,ignore.case=TRUE) )
matched_disease_abstract=apply(as.matrix(dieases),1,function(x) grep(x,abstract,ignore.case=TRUE) )
if(length(matched_disease_title)>0 | length(matched_disease_abstract)>0){
if(length(matched_disease_title)>0){
which_disease=which(matched_disease_title>0)
}else{
which_disease=which(matched_disease_abstract>0)
}
return(which_disease)
}else{
return(0)
}
if(which_disease>0){print(disease[which_disease])}
}
matched_diseases=apply(unique_gse,1,match_gse_disease)
matched_diseases_unlisted=as.matrix(unlist(lapply(matched_diseases, `[[`, 1)))
length(which(matched_diseases_unlisted>0))
507
tb=table(matched_diseases_unlisted)
names(tb)=c("NA",dieases)
tb
# NA Renal cell carcinoma Alzheimer’s disease Alzheimer Thyroid cancer
# 5795 22 10 13 13
# Dilated cardiomyopathy Colorectal cancer Prostate cancer Huntington’s disease Huntington
# 4 68 133 5 9
# Acute Myeloid Leukemia Pancreatic cancer Non-small cell lung cancer Glioma Parkinson’s disease
# 70 37 27 61 12
# Parkinson Type II diabetes mellitus Type 2 diabetes mellitus Chronic Myeloid Leukemia Endometrial cancer
# 8 1 6 4 4
#distinguish sample names
########## match additional terms
terms=read.table("87disease",header=FALSE)
terms=as.character(unlist((terms)))
terms=c(terms, dieases,"knock-out", "knock out", "knockout","siRNA","knockdown", "knock down", "knock-down", "crispr-i", "variant","pathway")
terms=unique(terms)
match_gse_terms<-function(gse_id){
print(gse_id)
tryCatch({
data <- getGEO(gse_id)
}, error = function(err) {
return(NULL)
}) # END tryCatch
title=data[[1]]@experimentData@title
abstract=data[[1]]@experimentData@abstract
matched_disease_title=apply(as.matrix(terms),1,function(x) grep(x,title,ignore.case=TRUE) )
matched_disease_abstract=apply(as.matrix(terms),1,function(x) grep(x,abstract,ignore.case=TRUE) )
if(length(matched_disease_title)>0 | length(matched_disease_abstract)>0){
if(length(matched_disease_title)>0){
which_disease=which(matched_disease_title>0)
}else{
which_disease=which(matched_disease_abstract>0)
}
return(disease[which_disease])
}else{
return(NULL)
}
if(which_disease>0){print(disease[which_disease])}
}
match_gse_terms2<-function(description,abstract){
matched_disease_title=apply(as.matrix(terms),1,function(x) grep(x,title,ignore.case=TRUE) )
matched_disease_abstract=apply(as.matrix(terms),1,function(x) grep(x,abstract,ignore.case=TRUE) )
if(length(matched_disease_title)>0 | length(matched_disease_abstract)>0){
if(length(matched_disease_title)>0){
which_disease=which(matched_disease_title>0)
}else{
which_disease=which(matched_disease_abstract>0)
}
return(disease[which_disease])
}else{
return(NULL)
}
if(which_disease>0){print(disease[which_disease])}
}
matched_terms=apply(unique_gse,1,match_gse_terms)
matched_terms_unlisted=as.matrix(unlist(lapply(matched_terms, `[[`, 1)))
length(which(matched_terms_unlisted>0))
1480
tb=table(matched_terms_unlisted)
names(tb)=c("NA",terms)
tb
#knockout siRNA crispr-i=>knockdown variant pathway
# 105 216 1 158 1000
save.image(file="15disease_parsed.RData")
data <- getGEO("GSE67492")
data$GSE67492_series_matrix.txt.gz@experimentData@title
data$GSE67492_series_matrix.txt.gz@experimentData@abstract
data[[1]]@phenoData@data$title
data[[1]]@phenoData@data$description
#
# > data[[1]]@phenoData@data$title
# V2 V3 V4 V5
# Idiopathic Dilated Cardiomyopathy 1 Idiopathic Dilated Cardiomyopathy 2 PAH with BMPR2 mutation 1 PAH with BMPR2 mutation 2
# V6 V7
# Control RV 1 Control RV 2
# 6 Levels: Control RV 1 Control RV 2 Idiopathic Dilated Cardiomyopathy 1 Idiopathic Dilated Cardiomyopathy 2 ... PAH with BMPR2 mutation 2
# > data[[1]]@phenoData@data$description
# V2 V3 V4 V5 V6 V7
# IDCC 1 IDCC 2 PPH SPH Control 1 Control 2
# Levels: Control 1 Control 2 IDCC 1 IDCC 2 PPH SPH
data <- getGEO(unique_gse[which(matched_diseases_unlisted>0)[2]])
data[[1]]@phenoData@data$title
c
#
# > data[[1]]@phenoData@data$title
# V2 V3
# PSC from PDA patient [CA2] PSC from PDA patient [CA3]
# V4 V5
# PSC from PDA patient [CA6] PSC from PDA patient [CA7]
# V6 V7
# PSC from non-cancer control [DI1] PSC from non-cancer control [DI2]
# V8 V9
# PSC from non-cancer control [DI3] PSC from non-cancer control [DI4]
# V10 V11
# PSC from non-cancer control [DI5] MiaPaCa-2 cells treated with DMEM [Mia-DMEM]
# V12 V13
# MiaPaCa-2 cells treated with calcipotriol [Mia-CAL] MiaPaCa-2 cells treated with conditioned media [Mia-CM]
# V14
# MiaPaCa-2 cells treated with conditioned media [Mia-CMS]
# 13 Levels: MiaPaCa-2 cells treated with calcipotriol [Mia-CAL] ... PSC from PDA patient [CA7]
# > data[[1]]@phenoData@data$description
# V2 V3
# processed data file available on Series record: CA.bw processed data file available on Series record: CA.bw
# V4 V5
# processed data file available on Series record: CA.bw processed data file available on Series record: CA.bw
# V6 V7
# processed data file available on Series record: DI.bw processed data file available on Series record: DI.bw
# V8 V9
# processed data file available on Series record: DI.bw processed data file available on Series record: DI.bw
# V10 V11
# processed data file available on Series record: DI.bw MiaPaCa-2 cells treated with DMEM
# V12 V13
# MiaPaCa-2 cells treated with calcipotriol MiaPaCa-2 cells treated with conditioned media
# V14
# MiaPaCa-2 cells treated with conditioned media
# 5 Levels: MiaPaCa-2 cells treated with calcipotriol MiaPaCa-2 cells treated with conditioned media ... processed data file available on Series record: DI.bw
#code that retrieves samples
#https://github.com/ctlab/phantasus/blob/master/R/loadGEO.R#L708
#################sort titles
group_samples<-function(titles){
library(stringdist)
library(igraph)
library(raster)
controls=NULL
controls=c(controls,grep("control",titles,ignore.case = TRUE))
controls=c(controls,grep("wild",titles,ignore.case = TRUE))
controls=c(controls,which(regexpr("[^a-z]wt[^a-z]",titles,ignore.case = TRUE) >0))
titles[controls]
if(length(controls)==0){
print("No control samples")
return(list())
}
###case
distm=as.matrix(stringdist::stringdistmatrix(titles[-controls],method="lv"))
colnames(distm)=titles[-controls]
rownames(distm)=titles[-controls]
distm
# s.a <- strsplit(titles[1], "")[[1]]
# s.b <- strsplit(titles[2], "")[[1]]
# paste(s.a[s.a != s.b], collapse = "")
distm[which(distm>1)]=0
g <- graph.adjacency(distm)
#plot(g)
clu <- components(g)
gr=igraph::groups(clu)
gr=gr[which(lengths(gr)>1)]
if(length(gr)==0){
print("No case samples")
return(list())
}
sample_groups=list()
for(i in 1:length(gr)){
#print(gr[[i]])
sample_groups<-c(sample_groups,list(gr[[i]]))
names(sample_groups)[i]=paste("case",i,sep="")
last_case=i
}
###control
distm=as.matrix(stringdist::stringdistmatrix(titles[controls],method="lv"))
colnames(distm)=titles[controls]
rownames(distm)=titles[controls]
distm
distm[which(distm>1)]=0
g <- graph.adjacency(distm)
#plot(g)
clu <- components(g)
gr=igraph::groups(clu)
gr=gr[which(lengths(gr)>1)]
if(length(gr)==0){
print("No control samples")
return(list())
}
for(i in 1:length(gr)){
#print(gr[[i]])
sample_groups<-c(sample_groups,list(gr[[i]]))
names(sample_groups)[last_case+i]=paste("control",i,sep="")
}
return(sample_groups)
}
group_samples2<-function(titles){
library(stringdist)
library(igraph)
library(raster)
controls=NULL
controls=c(controls,grep("control",titles,ignore.case = TRUE))
controls=c(controls,grep("wild",titles,ignore.case = TRUE))
controls=c(controls,which(regexpr("[^a-z]wt[^a-z]",titles,ignore.case = TRUE) >0))
titles[controls]
if(length(controls)==0){
print("No control samples")
return(list())
}
if(length(titles)-length(controls)==0){
print("No case samples")
return(list())
}
###case
titles_cases=titles[-controls]
rep_keys=get_rep_keys(titles_cases)
sample_groups=list()
last_case=1
if(length(rep_keys)>0){
for(i in 1:length(rep_keys)){
#print(gr[[i]])
matched=grep(rep_keys[i],titles_cases)
sample_groups<-c(sample_groups,list(titles_cases[matched]))
titles_cases=titles_cases[-matched]
names(sample_groups)[i]=paste("case",i,sep="")
last_case=i
}
}
if(length(titles_cases)>1){
distm=as.matrix(stringdist::stringdistmatrix(titles_cases,method="lv"))
colnames(distm)=titles_cases
rownames(distm)=titles_cases
distm
# s.a <- strsplit(titles[1], "")[[1]]
# s.b <- strsplit(titles[2], "")[[1]]
# paste(s.a[s.a != s.b], collapse = "")
distm[which(distm>1)]=0
g <- graph.adjacency(distm)
#plot(g)
clu <- components(g)
gr=igraph::groups(clu)
gr=gr[which(lengths(gr)>1)]
if(length(gr)==0&last_case==1){
print("No case samples")
return(list())
}
for(i in (last_case+1):length(gr)){
#print(gr[[i]])
sample_groups<-c(sample_groups,list(gr[[i]]))
names(sample_groups)[i]=paste("case",i,sep="")
}
}
###control
titles_controls=titles[controls]
rep_keys=get_rep_keys(titles_controls)
sample_groups=list()
last_control=1
if(length(rep_keys)>0){
for(i in 1:length(rep_keys)){
#print(gr[[i]])
matched=grep(rep_keys[i],titles_controls)
sample_groups<-c(sample_groups,list(titles_controls[matched]))
titles_controls=titles_controls[-matched]
names(sample_groups)[i]=paste("control",i,sep="")
last_control=i
}
}
if(length(titles_controls)>1){
distm=as.matrix(stringdist::stringdistmatrix(titles_controls,method="lv"))
colnames(distm)=titles_controls
rownames(distm)=titles_controls
distm
# s.a <- strsplit(titles[1], "")[[1]]
# s.b <- strsplit(titles[2], "")[[1]]
# paste(s.a[s.a != s.b], collapse = "")
distm[which(distm>1)]=0
g <- graph.adjacency(distm)
#plot(g)
clu <- components(g)
gr=igraph::groups(clu)
gr=gr[which(lengths(gr)>1)]
if(length(gr)==0&last_control==1){
print("No control samples")
return(list())
}
for(i in (last_control+1):length(gr)){
#print(gr[[i]])
sample_groups<-c(sample_groups,list(gr[[i]]))
names(sample_groups)[i]=paste("control",i,sep="")
}
}
return(sample_groups)
}
get_rep_keys<-function(query){
inferCondition <- sub("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(r)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\W|_)*", "", query, ignore.case = TRUE, perl = TRUE)
inferCondition2 <- sub("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*[^a-z]((rep.*)|(r)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\_)*", "", query, ignore.case = TRUE, perl = TRUE)
if(length(inferCondition)<inferCondition2){inferCondition=inferCondition2}
tb=as.data.frame(inferCondition) %>% group_by_all() %>% summarise(Unique_Elements = n())
uniques=tb[which(tb[,2]>1),1]
return(as.character(as.matrix(uniques)))
}
get_rep_keys2<-function(query){
#inferCondition <- sub("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(r)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\W|_)*", "", query, ignore.case = TRUE, perl = TRUE)
m=regexpr("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(r)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\W|_)*", query, ignore.case = TRUE, perl = TRUE)
inferCondition=apply(as.matrix(1:length(query)),1,function(x) substr(query[x],1,m[x]-1))
#inferCondition2 <- sub("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*[^a-z]((rep.*)|(r)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\_)*", "", query, ignore.case = TRUE, perl = TRUE)
m=regexpr("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*[^a-z]((rep.*)|(r)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\_)*", query, ignore.case = TRUE, perl = TRUE)
inferCondition2=apply(as.matrix(1:length(query)),1,function(x) substr(query[x],1,m[x]-1))
if(length(inferCondition)<length(inferCondition2)){inferCondition=inferCondition2}
tb=as.data.frame(inferCondition) %>% group_by_all() %>% summarise(Unique_Elements = n())
uniques=tb[which(tb[,2]>1),1]
return(as.character(as.matrix(uniques)))
}
get_rep_keys3<-function(query){
#inferCondition <- sub("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(r)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\W|_)*", "", query, ignore.case = TRUE, perl = TRUE)
m=regexpr("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*((rep.*)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\W|_)*", query, ignore.case = TRUE, perl = TRUE)
inferCondition=apply(as.matrix(1:length(query)),1,function(x) substr(query[x],1,m[x]-1))
nulls=which(inferCondition=="")
if(length(nulls)>0){inferCondition=inferCondition[-nulls]}
#inferCondition2 <- sub("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*[^a-z]((rep.*)|(r)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\_)*", "", query, ignore.case = TRUE, perl = TRUE)
m=regexpr("(?![-+}\\]\\)])(\\W|_)*((bio[A-z]*)|(tech[A-z]*))?[ .#_-]*[^a-zA-Z]((rep.*)|(r)|(set.*)|(sample)|(exp.*)|(case))[ .#_-]*\\d+(\\_)*", query, ignore.case = TRUE, perl = TRUE)
inferCondition2=apply(as.matrix(1:length(query)),1,function(x) substr(query[x],1,m[x]-1))
nulls=which(inferCondition2=="")
if(length(nulls)>0){inferCondition2=inferCondition2[-nulls]}
if(length(inferCondition)==0 & length(inferCondition2) ==0){return(NULL)}
if(length(inferCondition)<length(inferCondition2)){inferCondition=inferCondition2}
tb=as.data.frame(inferCondition) %>% group_by_all() %>% summarise(Unique_Elements = n())
uniques=tb[which(tb[,2]>1),1]
return(as.character(as.matrix(uniques)))
}
group_samples3<-function(gse,titles){
library(stringdist)
library(igraph)
library(raster)
controls=NULL
controls=c(controls,grep("control",titles,ignore.case = TRUE))
controls=c(controls,grep("wild",titles,ignore.case = TRUE))
controls=c(controls,grep("untreated",titles,ignore.case = TRUE))
controls=c(controls,which(regexpr("[^a-z]wt[^a-z]",titles,ignore.case = TRUE) >0))
pre_post_flag=0
if( length(which(regexpr("[^a-z]pre[^a-z]",titles,ignore.case = TRUE) >0))>0 & length(which(regexpr("[^a-z]post[^a-z]",titles,ignore.case = TRUE) >0))>0 ){
pre_post_flag=1
}
if(pre_post_flag){
controls=c(controls,which(regexpr("[^a-z]pre[^a-z]",titles,ignore.case = TRUE) >0))
}
titles[controls]
if(length(controls)==0){
print("No control samples")
return(list())
}else if(length(controls)==1){
print("Only one control sample")
return(list())
}
if(length(titles)-length(controls)==0){
print("No case samples")
return(list())
}else if(length(titles)-length(controls)==1){
print("Only one case sample")
return(list())
}
###case
titles_cases=titles[-controls]
rep_keys=get_rep_keys3(titles_cases)
sample_groups=list()
last_case=0
if(length(rep_keys)>0){
if(rep_keys!=""){
rep_keys=rep_keys[order(nchar(rep_keys), rep_keys,decreasing=TRUE)]
if(length(which(nchar(rep_keys)==0))){
rep_keys=rep_keys[-which(nchar(rep_keys)==0)]
}
for(i in 1:length(rep_keys)){
#print(gr[[i]])
rep_keys[i]=gsub("\\+","\\\\+",rep_keys[i])
rep_keys[i]=gsub("\\(","\\\\(",rep_keys[i])
rep_keys[i]=gsub("\\?","\\\\?",rep_keys[i])
rep_keys[i]=gsub("\\*","\\\\*",rep_keys[i])
rep_keys[i]=gsub("\\{","\\\\{",rep_keys[i])
rep_keys[i]=gsub("\\[","\\\\[",rep_keys[i])
rep_keys[i]=gsub("\\|","\\\\|",rep_keys[i])
matched=grep(rep_keys[i],titles_cases)
sample_groups<-c(sample_groups,list(titles_cases[matched]))
titles_cases=titles_cases[-matched]
names(sample_groups)[i]=paste("case",i,sep="")
last_case=i
}
}
}
if(length(titles_cases)>1){
distm=as.matrix(stringdist::stringdistmatrix(titles_cases,method="lv"))
colnames(distm)=titles_cases
rownames(distm)=titles_cases
distm
# s.a <- strsplit(titles[1], "")[[1]]
# s.b <- strsplit(titles[2], "")[[1]]
# paste(s.a[s.a != s.b], collapse = "")
distm[which(distm>1)]=0
g <- graph.adjacency(distm)
#plot(g)
clu <- components(g)
gr=igraph::groups(clu)
gr=gr[which(lengths(gr)>1)]
if(length(gr)==0&last_case==0){
print("No case samples")
return(list())
}else if(length(gr)>0){
for(i in 1:length(gr)){
#print(gr[[i]])
sample_groups<-c(sample_groups,list(gr[[i]]))
names(sample_groups)[length(sample_groups)]=paste("case",last_case+i,sep="")
}
}
}
###control
titles_controls=titles[controls]
rep_keys=get_rep_keys3(titles_controls)
last_control=0
if(length(rep_keys)>0){
if(rep_keys!=""){
rep_keys=rep_keys[order(nchar(rep_keys), rep_keys,decreasing=TRUE)]
if(length(which(nchar(rep_keys)==0))){
rep_keys=rep_keys[-which(nchar(rep_keys)==0)]
}
for(i in 1:length(rep_keys)){
#print(gr[[i]])
rep_keys[i]=gsub("\\+","\\\\+",rep_keys[i])
rep_keys[i]=gsub("\\(","\\\\(",rep_keys[i])
rep_keys[i]=gsub("\\?","\\\\?",rep_keys[i])
rep_keys[i]=gsub("\\*","\\\\*",rep_keys[i])
rep_keys[i]=gsub("\\{","\\\\{",rep_keys[i])
rep_keys[i]=gsub("\\[","\\\\[",rep_keys[i])
rep_keys[i]=gsub("\\|","\\\\|",rep_keys[i])
matched=grep(rep_keys[i],titles_controls)
sample_groups<-c(sample_groups,list(titles_controls[matched]))
titles_controls=titles_controls[-matched]
names(sample_groups)[length(sample_groups)]=paste("control",i,sep="")
last_control=i
}
}
}
if(length(titles_controls)>1){
distm=as.matrix(stringdist::stringdistmatrix(titles_controls,method="lv"))
colnames(distm)=titles_controls
rownames(distm)=titles_controls
distm
# s.a <- strsplit(titles[1], "")[[1]]
# s.b <- strsplit(titles[2], "")[[1]]
# paste(s.a[s.a != s.b], collapse = "")
distm[which(distm>1)]=0
g <- graph.adjacency(distm)
#plot(g)
clu <- components(g)
gr=igraph::groups(clu)
gr=gr[which(lengths(gr)>1)]
if(length(gr)==0&last_control==0){
print("No control samples")
return(list())
}else if(length(gr)>0){
for(i in 1:length(gr)){
#print(gr[[i]])
sample_groups<-c(sample_groups,list(gr[[i]]))
names(sample_groups)[length(sample_groups)]=paste("control",last_control+i,sep="")
}
}
}
sample_groups<-c(sample_groups,list(GSE=gse))
sample_groups<-c(sample_groups,list(titles=titles))
sample_groups<-c(sample_groups,list(total_sample_count=length(titles)))
sample_groups<-c(sample_groups,list(parsed_sample_count=length(unlist(sample_groups))-length(titles)-2))
return(sample_groups)
}
group_samples4<-function(gse,titles){
library(stringdist)
library(igraph)
library(raster)
tryCatch({
controls=NULL
controls=c(controls,grep("control",titles,ignore.case = TRUE))
controls=c(controls,grep("wild",titles,ignore.case = TRUE))
controls=c(controls,grep("untreated",titles,ignore.case = TRUE))
controls=c(controls,which(regexpr("[^a-z]wt[^a-z]",titles,ignore.case = TRUE) >0))
pre_post_flag=0
if( length(which(regexpr("[^a-z]pre[^a-z]",titles,ignore.case = TRUE) >0))>0 & length(which(regexpr("[^a-z]post[^a-z]",titles,ignore.case = TRUE) >0))>0 ){
pre_post_flag=1
}
if(pre_post_flag){
controls=c(controls,which(regexpr("[^a-z]pre[^a-z]",titles,ignore.case = TRUE) >0))
}
titles[controls]
if(length(controls)==0){
print("No control samples")
return(list())
}else if(length(controls)==1){
print("Only one control sample")
return(list())
}
if(length(titles)-length(controls)==0){
print("No case samples")
return(list())
}else if(length(titles)-length(controls)==1){
print("Only one case sample")
return(list())
}
###case
titles_cases=titles[-controls]
rep_keys=get_rep_keys3(titles_cases)
sample_groups=list()
last_case=0
if(length(rep_keys)>0){
if(rep_keys!=""){
rep_keys=rep_keys[order(nchar(rep_keys), rep_keys,decreasing=TRUE)]
if(length(which(nchar(rep_keys)==0))){
rep_keys=rep_keys[-which(nchar(rep_keys)==0)]
}
for(i in 1:length(rep_keys)){
#print(gr[[i]])
rep_keys[i]=gsub("\\+","\\\\+",rep_keys[i])
rep_keys[i]=gsub("\\(","\\\\(",rep_keys[i])
rep_keys[i]=gsub("\\?","\\\\?",rep_keys[i])
rep_keys[i]=gsub("\\*","\\\\*",rep_keys[i])
rep_keys[i]=gsub("\\{","\\\\{",rep_keys[i])
rep_keys[i]=gsub("\\[","\\\\[",rep_keys[i])
rep_keys[i]=gsub("\\|","\\\\|",rep_keys[i])
matched=grep(rep_keys[i],titles_cases)
sample_groups<-c(sample_groups,list(titles_cases[matched]))
titles_cases=titles_cases[-matched]
names(sample_groups)[i]=paste("case",i,sep="")
last_case=i
}
}
}
if(length(titles_cases)>1){
distm=as.matrix(stringdist::stringdistmatrix(titles_cases,method="lv"))
colnames(distm)=titles_cases
rownames(distm)=titles_cases
distm
# s.a <- strsplit(titles[1], "")[[1]]
# s.b <- strsplit(titles[2], "")[[1]]
# paste(s.a[s.a != s.b], collapse = "")
distm[which(distm>1)]=0
g <- graph.adjacency(distm)
#plot(g)
clu <- components(g)
gr=igraph::groups(clu)
gr=gr[which(lengths(gr)>1)]
if(length(gr)==0&last_case==0){
print("No case samples")
return(list())
}else if(length(gr)>0){
for(i in 1:length(gr)){
#print(gr[[i]])
sample_groups<-c(sample_groups,list(gr[[i]]))
names(sample_groups)[length(sample_groups)]=paste("case",last_case+i,sep="")
}
}
}
###control
titles_controls=titles[controls]
rep_keys=get_rep_keys3(titles_controls)
last_control=0
if(length(rep_keys)>0){
if(rep_keys!=""){
rep_keys=rep_keys[order(nchar(rep_keys), rep_keys,decreasing=TRUE)]
if(length(which(nchar(rep_keys)==0))){
rep_keys=rep_keys[-which(nchar(rep_keys)==0)]
}
for(i in 1:length(rep_keys)){
#print(gr[[i]])
rep_keys[i]=gsub("\\+","\\\\+",rep_keys[i])
rep_keys[i]=gsub("\\(","\\\\(",rep_keys[i])
rep_keys[i]=gsub("\\?","\\\\?",rep_keys[i])
rep_keys[i]=gsub("\\*","\\\\*",rep_keys[i])
rep_keys[i]=gsub("\\{","\\\\{",rep_keys[i])
rep_keys[i]=gsub("\\[","\\\\[",rep_keys[i])
rep_keys[i]=gsub("\\|","\\\\|",rep_keys[i])
matched=grep(rep_keys[i],titles_controls)
sample_groups<-c(sample_groups,list(titles_controls[matched]))
titles_controls=titles_controls[-matched]
names(sample_groups)[length(sample_groups)]=paste("control",i,sep="")
last_control=i
}
}
}
if(length(titles_controls)>1){
distm=as.matrix(stringdist::stringdistmatrix(titles_controls,method="lv"))
colnames(distm)=titles_controls
rownames(distm)=titles_controls
distm
# s.a <- strsplit(titles[1], "")[[1]]
# s.b <- strsplit(titles[2], "")[[1]]
# paste(s.a[s.a != s.b], collapse = "")
distm[which(distm>1)]=0
g <- graph.adjacency(distm)
#plot(g)
clu <- components(g)
gr=igraph::groups(clu)
gr=gr[which(lengths(gr)>1)]
if(length(gr)==0&last_control==0){
print("No control samples")
return(list())
}else if(length(gr)>0){
for(i in 1:length(gr)){
#print(gr[[i]])
sample_groups<-c(sample_groups,list(gr[[i]]))
names(sample_groups)[length(sample_groups)]=paste("control",last_control+i,sep="")
}
}
}
sample_groups<-c(sample_groups,list(GSE=gse))
sample_groups<-c(sample_groups,list(titles=titles))
sample_groups<-c(sample_groups,list(total_sample_count=length(titles)))
sample_groups<-c(sample_groups,list(parsed_sample_count=length(unlist(sample_groups))-length(titles)-2))
return(sample_groups)
}, error = function(err) {
return(list())