DoAbsolute | R Documentation |
An example can be found at README.
If calling for a sample failed, the error message will be written to
error.log
under result directory.
DoAbsolute(
Seg,
Maf = NULL,
sigma.p = 0,
max.sigma.h = 0.2,
min.ploidy = 0.5,
max.ploidy = 10,
primary.disease = NA,
platform = c("SNP_6.0", "Illumina_WES", "SNP_250K_STY"),
temp.dir = file.path(tempdir(), "Absolute"),
clean.temp = FALSE,
results.dir = getwd(),
max.as.seg.count = 1500,
max.non.clonal = 0.05,
max.neg.genome = 0.005,
copy.num.type = c("total", "allelic"),
min.mut.af = 0.1,
min.no.mut = 5,
verbose = FALSE,
nThread = 1L,
keepAllResult = TRUE,
recover = FALSE
)
Seg |
a |
Maf |
MAF, default is |
sigma.p |
Provisional value of excess sample level variance used for mode search. Default: 0 |
max.sigma.h |
Maximum value of excess sample level variance (Eq. 6). Default: 0.2 |
min.ploidy |
Minimum ploidy value to consider. Solutions implying lower ploidy values will be discarded. Default: 0.5 |
max.ploidy |
Maximum ploidy value to consider. Solutions implying greater ploidy values will be discarded. Default: 10 |
primary.disease |
Primary disease of the sample. Default: |
platform |
one of "SNP_6.0", "Illumina_WES", "SNP_250K_STY". Default: "SNP_6.0" |
temp.dir |
directory path used to store tempory files. Default: Absolute subdirectory under |
clean.temp |
if |
results.dir |
directory path used to store result files. Default: work directory |
max.as.seg.count |
Maximum number of allelic segments. Samples with a higher segment count will be flagged as 'failed'. Default: 1500 |
max.non.clonal |
Maximum genome fraction that may be modeled as non-clonal (subclonal SCNA). Solutions implying greater values will be discarded. Default: 0.05 |
max.neg.genome |
Maximum genome fraction that may be modeled as non-clonal with copy-ratio below that of clonal homozygous deletion. Solutions implying greater values will be discarded. Default: 0.005 |
copy.num.type |
The type of copy number to be handled. Either total or allelic. Total is what this package for. Default: "total" |
min.mut.af |
Minimum mutation allelic fraction. Mutations with lower allelic fractions will be filtered out before analysis. Default: 0.1 |
min.no.mut |
Minor allele frequency file, or NULL if one is not available. This specifies the data for somatic point mutations to be used by ABSOLUTE. Default: 5 |
verbose |
if |
nThread |
number of cores used for computation. Default: 1L |
keepAllResult |
if |
recover |
if |
ABSOLUTE is a famous software
developed by Broad Institute, however the RunAbsolute
function is designed for
computing one sample each time and set no default values. DoAbsolute help
user set default parameters according to ABSOLUTE documentation, provide an uniform interface to
input data easily and run RunAbsolute parallelly.
More detail about how to analyze ABSOLUTE results please see this link.
Shixiang Wang w_shixiang@163.com
Carter, Scott L., et al. "Absolute quantification of somatic DNA alterations in human cancer." Nature biotechnology 30.5 (2012): 413.
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