readSdrf {wrProteo} | R Documentation |
Read proteomics meta-data as sdrf file
Description
This function allows reading proteomics meta-data from sdrf file, as they are provided on https://github.com/bigbio/proteomics-sample-metadata. A data.frame containing all annotation data will be returned. To stay conform with the (non-obligatory) recommendations, columnnames are shown as lower caps.
Usage
readSdrf(
fi,
chCol = "auto",
urlPrefix = "github",
silent = FALSE,
callFrom = NULL,
debug = FALSE
)
Arguments
fi |
(character) main input; may be full path or url to the file with meta-annotation. If a short project-name is given,
it will be searched based at the location of |
chCol |
(character, length=1) optional checking of column-names |
urlPrefix |
(character, length=1) prefix to add to search when no complete path or url is given on |
silent |
(logical) suppress messages |
callFrom |
(character) allows easier tracking of messages produced |
debug |
(logical) display additional messages for debugging |
Details
The packages utils and wrMisc must be installed. Please note that reading sdrf files (if not provided as local copy) will take a few seconds, depending on the responsiveness of github.
Value
This function returns the content of sdrf-file as data.frame (or NULL
if the corresponding file was not found)
See Also
in read.table
Examples
## This may take a few sconds...
sdrf001819 <- readSdrf("PXD001819")
str(sdrf001819)