write.sgr: Write Affy IGB .sgr format files
In ACME: Algorithms for Calculating Microarray Enrichment (ACME)

Description Usage Arguments Author(s) Examples

The affy Integrated Genome Browser (IGB) is a powerful, fast browser for genomic data. The file format is simple (three columns: chromosome, location, and score) to generate. This function will write the sgr files associated with a aGFFcalc object. There will be either one or two files (default two) representing the raw data and the calculated data (which is output as -log10(val) for visualization purposes).

1	write.sgr(x, raw = TRUE, vals = TRUE, directory = ".")

`x`	An ACMESet or ACMECalcSet object
`raw`	Boolean. Create a file for the raw data?
`vals`	Boolean. Create a file for the calculated p-values?
`directory`	Give a directory for storing the files

Sean Davis

1 2	data(example.agff) write.sgr(example.agff)

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

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./testsamp1_raw.sgr 
./testsamp2_raw.sgr