From 16b4f55de1bee74c9f9060e6884d4d27c04cfe45 Mon Sep 17 00:00:00 2001
From: Efrain Gonzalez <egonz340@fiu.edu>
Date: Fri, 26 May 2017 12:18:30 -0400
Subject: [PATCH] wrong extension

---
 Rclean.txt | 198 -----------------------------------------------------
 1 file changed, 198 deletions(-)
 delete mode 100644 Rclean.txt

diff --git a/Rclean.txt b/Rclean.txt
deleted file mode 100644
index 788b9df..0000000
--- a/Rclean.txt
+++ /dev/null
@@ -1,198 +0,0 @@
-#Libraries required to run the code
-library(MASS)
-library(pryr)
-library(dplyr)
-library(tidyr)
-library(readr)
-library(stringr)
-
-
-#Necessary Functions
-#1#Function for handling the changing of row names and column names
-chngrownm <- function(mat){
-	row <- dim(mat)[1]
-	col <- dim(mat)[2]
-	j <- 1
-	x <- 1
-	p <- 1	
-	a <- 1
-	b <- 1
-	g <- 1
-	for(j in 1:col){
-		if("!Sample_source_name_ch1"==mat[1,j]){
-			colnames(mat)[j] <- "Brain_Region"	
-		} 
-		if("!Sample_title" == mat[1,j]){
-			colnames(mat)[j] <- "Title"
-		} 
-		if("!Sample_geo_accession" == mat[1,j]){
-			colnames(mat)[j] <- "ID_REF"
-		} else{
-			if(grepl("Sex|gender|Gender|sex",mat[2,j])==TRUE){
-				colnames(mat)[j] <- paste0("Sex",x)
-				x = x + 1
-			}
-			if(grepl("postmorteminterval|PMI|pmi",mat[2,j])==TRUE){
-				colnames(mat)[j] <- paste0("PMI",p)
-				p = p + 1
-			}
-			if(grepl("age|Age|AGE",mat[2,j])==TRUE){
-				colnames(mat)[j] <- paste0("Age",a)
-				a = a + 1
-			 }
-			if(grepl("braak|b&b",mat[2,j])==TRUE){
-				colnames(mat)[j] <- paste0("Braak",b)
-				b = b + 1
-			}
-			if(grepl("group|disease|control|AD|normal|diagnosis|Alzheimer|Control",mat[2,j])==TRUE){
-				colnames(mat)[j] <- paste0("Group",g)
-				g = g + 1
-			}
-			
-		}
-		j = j + 1
-	}
-	mat
-}			
-
-#2#Function for reorganizing information within the columns
-cinfo <- function(mat){
-	col <- dim(mat)[2]
-	j <-2
-	for(j in 2:col){
-		if(grepl("Group",colnames(mat)[j]) == TRUE){
-			mat[,j] <- gsub(".+:\\s|\\s.+;.+","",mat[,j])
-		}
-		if(grepl("Age",colnames(mat)[j])==TRUE){
-			mat[,j] <- gsub("\\D","",mat[,j])%>%
-				as.integer()
-		}
-		if(grepl("Sex",colnames(mat)[j])==TRUE){
-			mat[,j] <- gsub(".+:\\s","",mat[,j])
-		}
-		if(grepl("PMI",colnames(mat)[j])==TRUE){
-			mat[,j] <- gsub("[^0-9\\.]","",mat[,j])%>%
-				as.numeric() 
-		}
-		if(grepl("Braak",colnames(mat)[j])==TRUE){
-			mat[,j]<-gsub(".+:\\s","",mat[,j])%>%
-				as.roman()%>%
-				as.integer()
-		}
-	j=j+1
-	}
-	mat
-}
-
-#3#Function for changing the gene ID to gene name
-cgeneID <- function(GeneName,DATA){
-	colGene <- dim(GeneName)[2]
-	j <- 1
-	for(j in 1:colGene){
-		chngsreq <- grep(GeneName[1,j],DATA[1,])
-		DATA[1,chngsreq] <- gsub(GeneName[1,j],GeneName[2,j],DATA[1,chngsreq])
-		j = j+1
-	}
-	DATA
-}
-
-#4#Function for adjusting the gene names
-gcnames <- function(DiData,usecol=1){
-	nuruns <- dim(DiData)[2]
-	i = 1
-	nwnam <- rep("0",length.out=nuruns)
-	for(i in 1:nuruns){
-		if(length(strsplit(colnames(DiData)[i],"///")[[1]]) >= usecol){
-			nwnam[i]=strsplit(colnames(DiData)[i],"///")[[1]][usecol]
-		} else{
-			nwnam[i]=strsplit(colnames(DiData)[i],"///")[[1]][1]
-		}
-		
-	}
-	nwnam
-
-}
-
-
-
-#The Rest of this code will be used every time you want to change a data set
-
-#Getting the series matrix file
-print("Choose the series matrix file that you want to Analyze")
-alz <- file.choose()
-
-#Getting the GPL file
-print("Choose the GPL file that correlates with the above series matrix file")
-genena <- file.choose()
-
-
-#Set working directory based on the directory of the series matrix file
-##strsplit(alz,"[\\]") %>%
-##	.[[1]] %>%
-##	.[-length(.)] %>%
-##	paste(.,collapse="/") %>%
-##	setwd()
-	
-
-#Working with the wordy part of the document
-alzword <- alz %>%
-	read_delim(delim ="\t",comment = "!Series",col_names = FALSE)%>%
-	filter(grepl("!Sample",X1))%>%
-	filter(!grepl("!Sample_contact",X1))
-
-##Changing row names and column names:
-ALZWORD <- t(alzword)
-rownames(ALZWORD)=NULL
-colnames(ALZWORD) <- colnames(ALZWORD,do.NULL=FALSE)
-ALZWORD <- chngrownm(ALZWORD)[-1,]
-ALZWORD <- ALZWORD%>%
-	as.data.frame()%>%
-	dplyr::select(-starts_with("col"))
-
-##Reorganizing information within the columns
-ALZWORDF <- cinfo(ALZWORD)
-
-
-#Working with Actual Data part of file
-alzdat <- alz %>% 
-	read_delim(delim="\t",col_names=TRUE,comment = "!",skip=1)
-ALZDAT <- t(alzdat[,-1])
-rownames(ALZDAT)=NULL
-
-
-##Gene ID to Gene Name
-geneIDNam <- genena %>%
-	read_delim(delim="\t",comment = "#")%>%
-	dplyr::select(.,ID,grep("Symbol|ORF",colnames(.)))
-
-##Changing the ID to a Name
-ALZDAT1 <- cgeneID(t(geneIDNam),t(alzdat))
-colnames(ALZDAT) = ALZDAT1[1,]
-
-
-##Adjusting the column names aka the gene names
-colnames(ALZDAT) <- gcnames(ALZDAT)
-
-
-#Full Data
-Fullalzdw <- ALZDAT %>%
-	as.data.frame() %>%
-	cbind(ALZWORDF,.)
-
-##since the order in which the packages are added matters I moved this package to the top 
-##library(MASS)
-nfna <- strsplit(alz,"[\\]") %>%
-	.[[1]] %>%
-	.[length(.)] %>%
-	gsub("\\D","",.) %>%
-	c("GSE",.,"after.txt") %>%
-	paste(collapse = "")
-MASS::write.matrix(Fullalzdw,file = nfna,sep = "\t")
-#Perfect for excel viewing
-nfnaex <- strsplit(alz,"[\\]") %>%
-	.[[1]] %>%
-	.[length(.)] %>%
-	gsub("\\D","",.) %>%
-	c("GSE",.,"aftexcel.txt") %>%
-	paste(collapse = "")
-write.table(t(Fullalzdw), file = nfnaex, sep = "\t")
-- 
2.29.0