Description Usage Arguments Value See Also Examples
madloy check the median log R ratio(LRR) of all the MAD files specified or in a path to detect Loss of Y events. The LRR is computed by default for the autosomes and msY chrY:2694521-59034049 (hg19/GRCh37).
1 2 3 |
files |
A single file path (APT platform and MAD platform), a vector of file paths (MAD platform) or a MAD rawData folder path containing files ready to be processed with MAD (MAD platform). |
target.region |
The chromosome or region to be compared with the other regions. By default is the region chrY:2694521-59034049 (hg19/GRCh37) but it can be changed. |
ref.region |
If declared, the chromosome or region to be compared with the Y region in UCSC style (i.e. "chr21" or "chr21:1000-10000"). |
rsCol |
The position of the column with the SNP identifier. |
ChrCol |
The position of the column with the Chromosome field. |
PosCol |
The position of the column with the Position field. |
LRRCol |
The position of the column with the LRR identifier. |
trim |
trim the fraction (0 to 0.5) of probes to be trimmed when summaryzing LRR. By default is 0.05. |
offset |
median value of summarized LRR at target region |
mc.cores |
The number of cores used to perform the function. By default is set to 1. |
quiet |
Should the function not inform about the status of the process. By default is FALSE. |
... |
Other parameters. |
A MADloy object that contains the LRR means for all the files analyzed.
getLOY
to process results from MADloy
1 2 3 | ## Not run:
madloy(filepath, mc.cores=2)
## End(Not run)
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