import: Import raw file to an arrayCGH object

Description

Load raw data from a text file coming from image analysis and convert it to an arrayCGH object, using additional information about the array design.

Supported file types are Genepix Results file (.gpr), outputs from SPOT, or any text file with appropriate fields "Row" and "Column" and specified array design

Usage

import(file, var.names=NULL, spot.names=NULL, clone.names=NULL, type=c("default", "gpr", "spot"), id.rep=1, design=NULL, add.lines=FALSE, ...)

Arguments

file

a connection or character string giving the name of the file to import.

var.names

a vector of variables names used to compute the array design. If default is not overwritten, it is set to c("Block", "Column", "Row", "X", "Y") for gpr files, c("Arr.colx", "Arr.rowy", "Spot.colx", "Spot.rowy") for SPOT files, and c("Col", "Row") for other text files

spot.names

a list with spot-level variable names to be added to arrayCGH$arrayValues

clone.names

a list with clone-level variable names to be added to arrayCGH$cloneValues (only used in case of within-slide replicates)

type

a character value specifying the type of input file: currently .gpr files ("gpr"), spot files ("spot") and other text files with fields 'Col' and 'Row' ("default") are supported

id.rep

index of the replicate identifier (e.g. the name of the clone) in the vector(clone.names)

design

a numeric vector of length 4 specifying array design as number of blocks per column, number of blocks per row, number of columns by block, number of rows per block. This field is mandatory for "default" text files, optional for "gpr" files, and not used for "SPOT" files

add.lines

boolean value to handle the case when array design does not match number of lines. If TRUE, empty lines are added; if FALSE, execution is stopped

...

additional import parameters (e.g. 'sep=', or 'comment.char=', to be passed to read.delim function. Note that argument as.is=TRUE is always passed to read.delim, in order to avoid unapropriate conversion of character vectors to factors

Value

arrayCGH

Details

Mandatory elements of arrayCGH objects are the array design and the x and y absolute coordinates of each spot on the array. Output files from SPOT contain x and y relative coordinates of each spot within a block, as well as block coordinates on the array; one can therefore easily construct te corresponding arrayCGH object.

.gpr files currently only contain x and y relative coordinates of each spot within a block, and block index with no specification of the spatial block design: if block design is not specified by user, we compute it using the real pixel locations of each spot (X and Y variables in usual .gpr files)

If clone.names is provided, an additional data frame is created with clone-level information (e.g. clone names, positions, chromosomes, quality marks), aggregated from array-level information using the identifier specified by id.rep. This identifier is also added to the arrayCGH object created, with name 'id.rep'.

Due to space limitations, only the first 100 lines of sample 'gpr' and 'spot' files are given in the standard distribution of MANOR. Complete files are available at http://bioinfo.curie.fr/projects/manor/index.html

Examples

Run this code

dir.in <- system.file("extdata", package="MANOR")

## import from 'spot' files
spot.names <- c("LogRatio", "RefFore", "RefBack", "DapiFore", "DapiBack", "SpotFlag", "ScaledLogRatio")
clone.names <- c("PosOrder", "Chromosome")
edge <- import(paste(dir.in, "/edge.txt", sep=""), type="spot",
spot.names=spot.names, clone.names=clone.names, add.lines=TRUE) 

## import from 'gpr' files
spot.names <- c("Clone", "FLAG", "TEST_B_MEAN", "REF_B_MEAN",
"TEST_F_MEAN", "REF_F_MEAN", "ChromosomeArm")  
clone.names <- c("Clone", "Chromosome", "Position", "Validation")
  
ac <- import(paste(dir.in, "/gradient.gpr", sep=""), type="gpr",
spot.names=spot.names, clone.names=clone.names, sep="\t", 
comment.char="@", add.lines=TRUE)