data(ExomeCount)
ExomeCount <- ExomeCount[1:500,] ## small for the purpose of this test
ref_counts <- ExomeCount$Exome2 + ExomeCount$Exome3 + ExomeCount$Exome4
## creates a simple ExomeDepth object
## Note that I include the positions here (GRanges format)
## This is necessary for TestCNV to work
test_object <- new('ExomeDepth', test = ExomeCount$Exome1,
reference = ref_counts,
positions = ExomeCount)
## A positive control first
TestCNV (test_object, chromosome = 'chr1', start = 1387428, end = 1405539, type = 'deletion')
## And a region without evidence of call
TestCNV (test_object, chromosome = 'chr1', start = 987428, end = 1005539, type = 'deletion')
Run the code above in your browser using DataLab