read.perseus.default | R Documentation |
Read the custom Perseus matrix file format *.txt into R.
read.perseus.default(con, check = TRUE, additionalMatrices = FALSE) read.perseus.as.list(con, check = TRUE) read.perseus.as.matrixData(con, check = TRUE, additionalMatrices = FALSE) read.perseus.as.ExpressionSet(con, check = TRUE) read.perseus(con, check = TRUE, additionalMatrices = FALSE)
con |
A |
check |
Logical indicating whether to check for the validity of the exported object (slightly slower) |
additionalMatrices |
Logical indication whether to write out quality and imputation matrices in perseus format |
Defaults to a matrixData
object.
read.perseus.default
: Returns a list used internally to generate all other outputs
read.perseus.as.list
: Returns explicitly as a list
read.perseus.as.matrixData
: Returns explicitly as a specialized matrix data object
read.perseus.as.ExpressionSet
: Returns a bioconductor expression set object
Limitations to column names in R still apply. Column names valid in Perseus, such as 'Column 1' will be changed to 'Column.1'
If the provided connection con
is a character string, it will assumed
to be a file path. A connection
which is not seekable (see isSeekable
)
will be written to a temporary file. Any connection will be closed when read.perseus
exits.
read.perseus.as.list
, read.perseus.as.matrixData
and read.perseus.as.ExpressionSet
are also available depending on the class desired as an output
write.perseus
matrixData
tmp <- tempfile(fileext = ".txt") write('Column_1\tColumn_2\tColumn_3 #!{Description}\t\t #!{Type}E\tE\tE -1.860574\t-0.3910594\t0.2870352 NaN\t-0.4742951\t0.849998', file=tmp) mdata <- read.perseus(tmp)
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