read.perseus.default {PerseusR}

Read Perseus matrix files

Description

Read the custom Perseus matrix file format *.txt into R.

Usage

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)

Arguments

con

A connection object or the path to input file

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

Value

Defaults to a matrixData object.

Functions

• 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

Note

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

See Also

write.perseus

matrixData

Examples

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)