I have a directory with 144 files (.bed).
I would like to analyze them with a function from a R package (ChAseR). To avoid a for loop, I decided to use a lapply function.
# Define path
setwd("/home/works/Project/")
netpath="Table"
bedpath="Data/Naive_CD4_positive_T_Cells_BP/H3K27ac/bed_files"
# PCHiC contact network data loading and preprocessing
pchic=read.table(paste(netpath, "merged_samples_12Apr2015_full.txt", sep="/"), sep="\t", skip=4, header=T)
pchic[,1]=paste('chr', pchic[,1], sep='')
pchic[,6]=paste('chr', pchic[,6], sep='')
Tcellnaive <- pchic[which(pchic$Naive_CD4>=5),c(1,2,3,6,7,8)]
tnet=chaser::make_chromnet(Tcellnaive)
# Load histone modifications data from Chen et al. 2016 (doi: 10.1016/j.cell.2016.10.026)
files <- list.files(path=bedpath, pattern="*.bed", full.names=TRUE, recursive=FALSE)
tnet2 <- lapply(files, chaser::load_features(tnet, files, type="macs2", missingv=0, featnames="H3K27ac"))
I obtained this message:
reading from file Data/Naive_CD4_positive_T_Cells_BP/H3K27ac/bed_files/S01342H2.H3K27ac.ppqt_macs2_wp10.20150819.bed...
reading from file Data/Naive_CD4_positive_T_Cells_BP/H3K27ac/bed_files/S0137XH3.H3K27ac.ppqt_macs2_wp10.20150819.bed...
reading from file Data/Naive_CD4_positive_T_Cells_BP/H3K27ac/bed_files/S013CNH3.H3K27ac.ppqt_macs2_wp10.20150819.bed...
reading from file Data/Naive_CD4_positive_T_Cells_BP/H3K27ac/bed_files/S013DLH2.H3K27ac.ppqt_macs2_wp10.20150819.bed...
Error in file(file, "rt") : invalid 'description' argument
How to resolve this error? Maybe a problem with the path or the function?
Related
Fresh lettuce here so don't laugh at my questions:
Say I have a folder containing 40 individual .txt files and I would like to convert them into .csv format.
To have an end product : a new folder with 40 individual .csv files.
I have seen similar question posted and their code, however the code did run but the .csv files is nothing like the orginal .txt file: all the data are scrambled.
Since I want to keep the header, and I want to read all the data/rows in the .txt file. I made some cosmetic changes to the code, still didnt run and returned a warning "Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'C:/Users/mli/Desktop/All TNFa controls in the training patients ctrl_S1018263__3S_TNFaCHx_333nM+0-1ugml_none.txt': Invalid argument"
My code as below:
directory <- "C:/Users/mli/Desktop/All TNFa controls in the training patients"
ndirectory <- "C:/Users/mli/Desktop/All TNFa controls in the training patients/CSV"
file_name <- list.files(directory, pattern = ".txt")
files.to.read <- paste(directory, file_name, sep="\t")
files.to.write <- paste(ndirectory, paste0(sub(".txt","", file_name),".csv"), sep=",")
for (i in 1:length(files.to.read)) {
temp <- (read.csv(files.to.read[i], sep="\t", header = T))
write.csv(temp, file = files.to.write[i])
}
When you paste your path with the name of your file at line 4 and 5, use /, to obtain a new path in a character string. The sep value is what the function will put when it will paste together multiple strings.
> paste('hello','world',sep=" ")
[1] "hello world"
> paste('hello','world',sep="_")
[1] "hello_world"
This is different of the sep value you need in read.csv that define the character between each column of you csv file.
I would like to unzip and read in a shape file from the web in R without relying on rgdal. I found the read.shp function of the fastshp package that can apparently accomplish this without rgdal installed in the environment, however, I'm having trouble implementing.
I would like a function that can unzip and then read in the shape file akin to what's found in this SO post but for the read.shp function. I tried the following but to no avail:
dlshape=function(shploc, format) {
temp=tempfile()
download.file(shploc, temp)
unzip(temp)
shp.data <- sapply(".", function(f) {
f <- file.path(temp, f)
return(read.shp(".", format))
})
}
shp_object<-dlshape('https://www2.census.gov/geo/tiger/TIGER2017/COUNTY/tl_2017_us_county.zip', 'polygon')
Error in read.shp(".", format) : unused argument (format)
I also tried the following:
dlshape=function(shploc) {
temp=tempfile()
download.file(shploc, temp)
unzip(temp)
shp.data <- sapply(".", function(f) {
f <- file.path(temp, f)
return(read.shp("."))
})
}
shp_object<-dlshape('https://www2.census.gov/geo/tiger/TIGER2017/COUNTY/tl_2017_us_county.zip')
Error in file(shp.name, "rb") : cannot open the connection
In addition: Warning messages:
1: In file(shp.name, "rb") : 'raw = FALSE' but '.' is not a regular file
2: In file(shp.name, "rb") :
Show Traceback
Rerun with Debug
Error in file(shp.name, "rb") : cannot open the connection
I suspect it has to do with the fact that in the function read.shp() I'm feeding it the folder name and not the .shp name (for readOGR that works but not for read.shp). Any assistance is much appreciated.
You can use unzip() from utils and read_sf() from sf to unzip and then load your shapefile. Here is a working example:
# Create temp files
temp <- tempfile()
temp2 <- tempfile()
# Download the zip file and save to 'temp'
URL <- "https://www2.census.gov/geo/tiger/TIGER2017/COUNTY/tl_2017_us_county.zip"
download.file(URL, temp)
# Unzip the contents of the temp and save unzipped content in 'temp2'
unzip(zipfile = temp, exdir = temp2)
# Read the shapefile. Alternatively make an assignment, such as f<-sf::read_sf(your_SHP_file)
sf::read_sf(temp2)
I'm a bit stuck with this code... The purpose is to read only text files from a folder with few different kind of files, take a column for each one and create a data frame with every extracted column (cbind.fill is a hand-made function that add a new column and fill the "empty" spaces with NA values). Here is the code:
setwd("...folderOfInterest/")
genes_data <- data.frame()
for(i in list.files(pattern = "^GO_.*txt", full.names = TRUE)){
print(i) #this works perfectly, it only prints desired files...
q <- read.table(i, header = TRUE, sep = "\t", quote = NULL)
genes_data <- cbind.fill(genes_data, q[,2])
}
As #Adam B suggests, here is the print(i) output and a screenshot of the folder (folder_screenshot):
[1] "./GO_ALPHA_AMINO_ACID_CATABOLIC_PROCESS.xls"
[1] "./GO_ALPHA_AMINO_ACID_METABOLIC_PROCESS.xls"
[1] "./GO_ALPHA_BETA_T_CELL_ACTIVATION.xls"
[1] "./GO_AMINO_ACID_BETAINE_METABOLIC_PROCESS.xls"
[1] "./GO_AMINO_ACID_IMPORT.xls"
[1] "./GO_AMINO_ACID_TRANSMEMBRANE_TRANSPORT.xls"
[1] "./GO_AMINO_ACID_TRANSPORT.xls"
[1] "./GO_AMINOGLYCAN_BIOSYNTHETIC_PROCESS.xls"
[1] "./GO_ANGIOGENESIS.xls"
[1] "./GO_ANION_TRANSPORT.xls"
[1] "./GO_ANTIGEN_PROCESSING_AND_PRESENTATION.xls"
[1] "./GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_ENDOGENOUS_ANTIGEN.xls"
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file './GO_ANTIGEN_PROCESSING_AND_PRESENTATION_OF_ENDOGENOUS_ANTIGEN.xls': No such file or directory
(note: the files' extension is .xls, but really they are .txt files)
It propmts this message:
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file './GO_ANTIGEN_PROCESSING_AND_PRESENTATION.txt': No such file or directory
Also running only q <- read.table(i, header = TRUE, sep = "\t", quote = NULL) appears this error message.
I think I'm in the correct folder (because print(i) works good), I've also changed full.names option and set list.files as a variable out the loop... but nothins seems to work. Please, if anybody has an idea it'll be welcome!
I've tried it on randomly generated files and it works. You probably do not need to cd into the directory with the data, just give the list.files a dir argument with the path to your data directory.
GOfls <- list.files("indata", pattern = "^GO_.*\\.txt", full.names = TRUE)
head(GOfls)
[1] "indata/GO_amswylfbgp.txt" "indata/GO_amswylfbgptxt" "indata/GO_apqqqktvir.txt"
[4] "indata/GO_arwudmbzsr.txt" "indata/GO_autljyljgn.txt" "indata/GO_beeqcmnayk.txt"
# lapply -> do.call for reading and binding the data is better approach
gene_data <- do.call('cbind', lapply(GOfls, function(path) read.delim(path)[,2]))
# have a look at the data
dim(gene_data)
[1] 100 100
I have tried to reproduce your problem this way (it's optional text):
dir.create("indata")
fls <- lapply(1:100, function(i) data.frame(matrix(rnorm(1000), ncol = 10)))
names(fls) <- replicate(100, paste0("./indata/", "GO_",
paste0(sample(letters, 10, replace = T),
collapse = ""), ".txt"
)
)
lapply(names(fls), function(x) write.table(fls[[x]], x, quote = F, sep = "\t"))
head(dir("indata"))
[1] "GO_acebruujkw.pdf" "GO_amswylfbgp.txt" "GO_amswylfbgptxt" "GO_apqqqktvir.txt"
[5] "GO_arwudmbzsr.txt" "GO_autljyljgn.txt"
# I have added some renamed .txt files (.pdf, .tiff, .gel) to the indata
rm(list = ls())
That's solved! It's a bit strange but copying the folder of interest into the desktop the code seems to work again.
A mate and I saw that hard disk's activity was collapsed, so we thought that maybe there could be a problem in the process of reading... so copying the folder was the (simple) solution!
Nevertheless, if anybody has an idea that explains this strange situation I'm sure it'll be useful! Thanks a lot!
EDIT
I've done some tests and maybe the problem is the name of the folder path, which it'd too long and crashes the loop.
I think it's because you're searching for .xls files, but then trying to open it at as a .txt file
In excel try saving the files as comma or tab delimited text files.
If you want to open excel files directly they have a few packages that can do that. Try readxl.
I am new to programming.Currently doing R programming in coursera and got this error while doing assignment named "pollutantmean".I searched in forums and stackoverflow,but couldnt able to fix it.Appreciate your help.Thanks.
I got this error :
Error in file(file, "rt") : cannot open the connection In addition: Warning message:
In file(file, "rt") : cannot open file 'NA': No such file or directory
Note: I have a folder "specdata" which is the working directory.This "specdata" has all the 332 csv files.I want to calculate mean for one of the pollutant column named "pollutant" in those files and "directory" is the location of those files."id" is a integer vector mentioning the monitor number.so,here is my code:
pollutantmean <- function(directory, pollutant, id = 1:332) {
files_full <- list.files(directory, full.names = TRUE)
dat <- data.frame()
for (i in id) {
dat <- rbind(dat, read.csv(files_full[i]))
}
mean(dat[, pollutant], na.rm = TRUE)
}
pollutantmean("specdata","sulfate",id = 1:10)
As per the error, it seems that list.files is returning empty vector for files names.
list.files returns only file nam inside the directory by default. So in that case, you should set the working directory first, so that read.csv will read the files inside the working directory.
setwd("<directory name>")
Now your function should work fine.
I have script as below:
setwd ("I:/prep/Coord/RData/test")
#load .csv files
a.files <- grep("^Whirr", dir(), value=TRUE) #pattern matching
b.files <- paste0("Files_", a.files)
for(i in length(a.files)){
a <- read.table(a.files[i], header=T, sep=",", row.names=1) #read files start with Whirr_
b <- read.table(b.files[i], header=T, sep=",", row.names=1) #read files start with Files_
a
b
cr <- as.matrix(a) %*% as.matrix(t(a)
cr
diag(cr)<-0
cr
#write to file
write.csv(cr, paste0("CR_", a.files[i], ".csv"))
}
Basically, what I want to do is to compare two files which have similar filename at the end of file name, and do the calculation, and write the result to file.
When I tried to print a.files and b.files, the output seems ok for me. The output as below:
> a.files <- grep("^Whirr", dir(), value=TRUE) #pattern matching
> b.files <- paste0("Files_", a.files, sep="")
Error: could not find function "paste0"
> a.files
[1] "Whirr_127.csv" "Whirr_128.csv"
> b.files
[1] "Files_ Whirr_127.csv" "Files_ Whirr_128.csv"
>
I tried to feed the script with multiple files, but I got an error msg as below:
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") : cannot open file 'Files_ Whirr_128.csv': No such file or directory
So, I tried to use file.choose, but it also doesn't work for me.
Appreciate help from the expert
Change the line:
b.files <- paste0("Files_", a.files)
to:
b.files <- paste("Files_", a.files, sep="")
You are using a version of R that does not have paste0 (I see that code was given to you in an earlier answer). This means you were keeping an earlier version of b.files, perhaps one that had been constructed using paste.
One important lesson about this is that whenever you get an error message about a line, such as Error: could not find function "paste0", that means the line did not happen! You have to fix that error before you paste the code, or tell us about the error when you do- otherwise we assume the b.files <- paste0("Files_", a.files) line works.