Hi,
At present, the minfi 1.13.1 read.450k.exp function can result in an erroneous
file path when reading in IDAT files using a targets file.
The following line of code can create a path where "base" is repeated as
"targets$Basename" already contains "base" if read.450k.sheet was used to
create "targets":
files <- file.path(base, targets$Basename)
This results in an error when trying to read in the files:
rgSet <- read.450k(files, extended = extended, verbose = verbose)
This is an example of the error:
Error: processing vignette 'minfi.Rnw' failed with diagnostics:
chunk 7 (label = paths)
Error in read.450k(files, extended = extended, verbose = verbose) :
The following specified files do not
exist:/home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646052/5723646052_R02C02_Grn.idat,
/home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646052/5723646052_R04C01_Grn.idat,
/home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646052/5723646052_R05C02_Grn.idat,
/home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646053/5723646053_R04C02_Grn.idat,
/home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata//home/biocbuild/bbs-3.1-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat,
/home/biocbuild/bbs-3.1-bioc/R
Execution halted
This is currently affecting the development version of minfi and any other
packages that are using minfi functions to read in methylation data.
Regards,
Jovana Maksimovic
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