Alternative for wininet method in tximeta
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uhlkatie • 0
@uhlkatie-20770
Last seen 24 days ago
United States

I am relatively new to RNA-seq analysis, so I have been following the DESEQ2 tutorial with some sample human data. I attempted to use the "tximeta" function to create a summarized experiment, but I was met with the following error:

library(tximeta)
se <- tximeta(coldata)

importing quantifications
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
found matching transcriptome:
[ GENCODE - Homo sapiens - release 39 ]
useHub=TRUE: checking for TxDb via 'AnnotationHub'
snapshotDate(): 2022-04-21
did not find matching TxDb via 'AnnotationHub'
building TxDb with 'GenomicFeatures' package
Import genomic features from the file as a GRanges object ... Error in download.file(resource(con), destfile) :
the 'wininet' method for ftp:// URLs is defunct


It seems that the problem is that 'wininet' no longer works to retrieve the files. I also tried this method:

library("tximport")
library("tximportData")

Error in file(file, "rt") : cannot open the connection


The .csv file does not exist in my folders, but I'm not sure how to get it. Does anyone know of an alternative method for the wininet so that tximeta will work? Is there any way to tell tximeta to use a different way of opening files? Any advice would be much appreciated.

DESeq2 tximport tximportData tximeta • 144 views
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@mikelove
Last seen 2 days ago
United States

Try installing the curl package (from CRAN).

I'm not sure if just installing will do the trick. What version of R do you have?

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Hello,

I have R version 4.2.1. I was able to install the curl package successfully. I received the same error message when I tried to run the code.

library(tximeta)
library(curl)
se <- tximeta(coldata)

importing quantifications
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
found matching transcriptome:
[ GENCODE - Homo sapiens - release 39 ]
useHub=TRUE: checking for TxDb via 'AnnotationHub'
C:\Users\lilab\AppData\Local/R/cache/R/AnnotationHub
does not exist, create directory? (yes/no):  yes
|====================================================================| 100%

snapshotDate(): 2022-04-21
did not find matching TxDb via 'AnnotationHub'
building TxDb with 'GenomicFeatures' package
Import genomic features from the file as a GRanges object ... Error in download.file(resource(con), destfile) :
the 'wininet' method for ftp:// URLs is defunct

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Entering edit mode

I think you can then change the ?options

e.g.

options(download.file.method = "libcurl")

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This worked perfectly. Thank you!