processMAD | R Documentation |
Process a MAD file to retrieve the median log R ratio of a region of interest.
processMAD(file, query, rsCol, ChrCol, PosCol, LRRCol, trim = 0.1)
file |
File path of the MAD file to be processed. |
query |
Region of interest to check the LRR in rangedData format. |
rsCol |
Column of the MAD file with the name of the SNP. |
ChrCol |
Column of the MAD file with the chromosome information. |
PosCol |
Column of the MAD file with the position information. |
LRRCol |
Column of the MAD file with the LRR information. |
trim |
the fraction (0 to 0.5) of probes to be trimmed when summaryzing LRR. This argument tries to control the effect of having CNVs across genome. Default is 0.1. |
A list with the mean of the LRR for the query value.
## Not run:
processMAD(file=file.path, query=rangedDataROI, rsCol=2, chrCol=3, PosCol=4, LRRCol=5)
## End(Not run)
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