readPairs: Read Nimblegen .pair files

In HELP: Tools for HELP data analysis

Description

Function to extract data from corresponding files in the Nimblegen .pair format.

Usage

readPairs(x, y, z, ...)

Arguments

x	the name of the file containing data from signal channel 1. Each line of the file is interpreted as a single data point. If it does not contain an absolute path, the file name is relative to the current working directory, getwd(). Tilde-expansion is performed where supported. Alternatively, x can be a readable connection (which will be opened for reading if necessary, and if so closed at the end of the function call). x can also be a complete URL.
y	the name of the file containing data from signal channel 1. Each line of the file is interpreted as a single data point. If it does not contain an absolute path, the file name is relative to the current working directory, getwd(). Tilde-expansion is performed where supported. Alternatively, y can be a readable connection (which will be opened for reading if necessary, and if so closed at the end of the function call). y can also be a complete URL.
z	object in which to store pair information from files. Can be an ExpressionSet, in which case pair data will be stored in featureData.
...	Arguments to be passed to methods (see readPairs-methods): name character input specifying a sample name to assign to the data from specified pair files. If NULL (default), a value will be extracted from the filename specified in x. element.x which element of AssayData (default is "exprs") in which to store signal channel 1 data. element.y which element of AssayData (default is "exprs2") in which to store signal channel 2 data. match.probes logical specifying whether to match data from pair files by "PROBE\_ID" with any pre-existing data. if TRUE (default), order of values will be rearranged so long as there are already "PROBE\_ID"s specified in featureData. path a character vector containing a single full path name to which filenames will be appended. If NULL, filenames (x and y) are treated as is. comment.char character: a character vector of length one containing a single character or an empty string (default is "\#"). Use "" to turn off the interpretation of comments altogether. sep the field separator character (default is "\t"). Values on each line of the file are separated by this character. If sep = "" the separator is "white space", that is one or more spaces, tabs, newlines or carriage returns. quote the set of quoting characters (default is "\""). To disable quoting altogether, use quote = "". See scan for the behaviour on quotes embedded in quotes. Quoting is only considered for columns read as character, which is all of them unless colClasses is specified. eSet ExpressionSet input (default is new("ExpressionSet")) in which to store pair information in assayData verbose logical; if TRUE (default) progress will be output to screen. If FALSE, no output will be displayed. \dots other arguments to be passed to read.table. See read.table.

Value

Returns an ExpressionSet filled with assayData containing matrices of data from both signal channels.

and featureData containing the following featureColumns:

SEQ_ID	a vector of characters with container IDs, linking each probe to a parent identifier
PROBE_ID	a vector of characters containing unique ID information for each probe

and phenoData containing the following sampleColumns:

CHIPS	a vector of characters with .pair file locations for signal channel 1 data
CHIPS2	a vector of characters with .pair file locations for signal channel 2 data

Author(s)

Reid F. Thompson ([e-mail])

See Also

readPairs-methods, read.table

Examples

#demo(pipeline,package="HELP")

x <- 1:500
y <- rev(x)
data <- sample(8000:10000/1000,size=500)
seqids <- sample(1:50,size=500,replace=TRUE)
cat("#COMMENT\nSEQ_ID\tPROBE_ID\tX\tY\tPM\n",file="./read.pair.test.1")
table.1 <- cbind(seqids,y,x,x,data)
write.table(table.1,file="./read.pair.test.1",append=TRUE,col.names=FALSE,row.names=FALSE,quote=FALSE,sep="\t")
cat("#COMMENT\nSEQ_ID\tPROBE_ID\tX\tY\tPM\n",file="./read.pair.test.2")
table.2 <- cbind(seqids,y,x,x,rev(data))
write.table(table.2,file="./read.pair.test.2",append=TRUE,col.names=FALSE,row.names=FALSE,quote=FALSE,sep="\t")
x <- readPairs("./read.pair.test.1","./read.pair.test.2")
c(seqids[1],y[1],data[1],rev(data)[1])
pData(featureData(x))$"SEQ_ID"[1]
pData(featureData(x))$"PROBE_ID"[1]
assayDataElement(x, "exprs")[1]
assayDataElement(x, "exprs2")[1]

#rm(table.1,table.2,x,y,data,seqids)
#file.remove("./read.pair.test.1")
#file.remove("./read.pair.test.2")

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[1]  32.000 500.000   9.246   8.437
[1] 32
50 Levels: 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 ... 9
[1] 500_1_1
500 Levels: 100_401_401 101_400_400 102_399_399 103_398_398 ... 9_492_492
[1] 9.246
[1] 8.437

HELP documentation built on Nov. 8, 2020, 11:08 p.m.