Description Usage Arguments Details Value Author(s) Examples
Simulate bulk sequencing data by taking a local sample from the tumor and computing the variant allele frequencies of the various mutations.
1 2 3 4 5 6 7 | randomBulkSamples(
tumor,
nsamples,
cube.length = 5,
threshold = 0.05,
coverage = 0
)
|
tumor |
A list which is the output of |
nsamples |
The number of bulk samples to take. |
cube.length |
The side length of the cube of cells to be sampled. |
threshold |
Only mutations with an allele frequency greater than the threshold will be included in the sample. |
coverage |
If nonzero then deep sequencing with specified coverage is performed. |
This is the same as bulkSample()
, except multiple samples are taken
with random center points.
A data frame with nsamples
rows and columns corresponding to the mutations.
The entries are the mutation allele frequency.
Phillip B. Nicol
1 2 | out <- simulateTumor(max_pop = 1000)
df <- randomBulkSamples(tumor = out, nsamples = 5, cube.length = 5, threshold = 0.05)
|
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