write.table: Write summary of the significant regions to a table
In KCsmart: Multi sample aCGH analysis package using kernel convolution

Description Usage Arguments Details Author(s) See Also Examples

Write summary of the significant regions to a table

write.table(x, file = "", append = FALSE, quote = TRUE, sep = " ",
                 eol = "\n", na = "NA", dec = ".", row.names = TRUE,
                 col.names = TRUE, qmethod = c("escape", "double"), fileEncoding = "")
## S4 method for signature 'sigSegments'
write.table(x, file="", append = FALSE, quote = 7, sep = "\t", eol = "\n", na = "NA", dec = ".", row.names = TRUE, col.names=c("Status", "Chromosome", "Start", "End", "Average KC score", "Mode KC score", "Probes"), qmethod = c("escape", "double"))
## S4 method for signature 'compKcSigRegions'
write.table(x, file="", append = FALSE, quote = 7, sep = "\t", eol = "\n", na = "NA", dec = ".", row.names = FALSE, col.names=c("startrow", "endrow", "chromosome", "startposition", "endposition"), qmethod = c("escape", "double"))

`x`	The sigSegments object to be summarized
`file`	either a character string naming a file or a connection open for writing. '""' indicates output to the console.
`append`	logical. Only relevant if 'file' is a character string. If 'TRUE', the output is appended to the file. If 'FALSE', any existing file of the name is destroyed.
`quote`	a logical value ('TRUE' or 'FALSE') or a numeric vector. If 'TRUE', any character or factor columns will be surrounded by double quotes. If a numeric vector, its elements are taken as the indices of columns to quote. In both cases, row and column names are quoted if they are written. If 'FALSE', nothing is quoted.
`sep`	the field separator string. Values within each row of 'x' are separated by this string.
`eol`	the character(s) to print at the end of each line (row).
`na`	the string to use for missing values in the data.
`dec`	the string to use for decimal points in numeric or complex columns: must be a single character.
`row.names`	either a logical value indicating whether the row names of 'x' are to be written along with 'x', or a character vector of row names to be written.
`col.names`	either a logical value indicating whether the column names of 'x' are to be written along with 'x', or a character vector of column names to be written. See the section on 'CSV files' for the meaning of 'col.names = NA'.
`qmethod`	a character string specifying how to deal with embedded double quote characters when quoting strings. Must be one of '"escape"' (default), in which case the quote character is escaped in C style by a backslash, or '"double"', in which case it is doubled. You can specify just the initial letter.
`fileEncoding`	character string: if non-empty declares the encoding to be used on a file (not a connection) so the character data can be re-encoded as they are written. See `file`.

Writes a summary of the sigSegments object to file. The resulting table contains 7 columns. The interpretation of the columns is as follows:

Status Either 'L' for loss or 'G' for gain
Chromosome The chromosome on which this segment is located
Start The start position (in base pairs) of the segment on the chromosome
End The end position of the segment on the chromosome
Average KC scoreThe average KCsmart score over all base pairs in this segment
Mode KC scoreThe highest (for gains) or lowest (for losses) KCsmart score over all base pairs in this segment
Probes All probes from the original data that fall into this segment

Jorma de Ronde

calcSpm, getSigSegments

data(hsSampleData)
data(hsMirrorLocs)

spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)

siglevel1mb <- findSigLevelTrad(hsSampleData, spm1mb, n=3)

sigSegments1mb <- getSigSegments(spm1mb, siglevel1mb)
write.table(sigSegments1mb, file=file.path(tempdir(),'sigSegments1mb.txt'))