This function imports user-defined sample metadata saved in a spreadsheet.
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Required column names. The
"description" column is always required, and
must match the bcbio per sample directory names exactly. Inclusion of the
"fileName" column isn't required but is recommended for data provenance.
Note that some bcbio examples on readthedocs use
"samplename" (note case)
"fileName". This function checks for that and will rename the
"fileName" automatically. We're using the
(note case) to define unique sample names, in the event that bcbio has
processed multiplexed samples.
Demultiplexed samples. The samples in the bcbio run must map to the
"description" column. The values provided in description for demultiplexed
samples must be unique. They must also be syntactically valid, meaning that
they cannot contain illegal characters (e.g. spaces, non-alphanumerics,
dashes) or begin with a number. Consult the documentation in
help(topic = "make.names") for more information on valid names in R.
Multiplexed samples. This applies to some single-cell RNA-seq formats,
including inDrops. In this case, bcbio will output per-sample directories
with this this structure:
readSampleData() checks to
see if the
"description" column is unique. If the values are duplicated,
the function assumes that bcbio processed multiplexed FASTQs, where multiple
samples of interest are barcoded inside a single FASTQ. This this case, you
must supply additional
Note that bcbio currently outputs the reverse complement index sequence in
the sample directory names (e.g.
"sample-ATAGAGAG"). Define the forward
index barcode in the
sequence column here, not the reverse complement. The
reverse complement will be calculated automatically and added as the
revcomp column in the sample metadata.
Works with local or remote files.
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## Demultiplexed ==== file <- file.path(basejumpTestsURL, "bcbio-metadata-demultiplexed.csv") x <- importSampleData(file, pipeline = "bcbio") print(x) ## Multiplexed ==== file <- file.path(basejumpTestsURL, "bcbio-metadata-multiplexed-indrops.csv") x <- importSampleData(file, pipeline = "bcbio") print(x)
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