ABSOLUTE 사용법
설치
환경에 R 설치
$ conda install -c r r
Shell
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NumDeriv 패키지 설치
# in R
install.packages("numDeriv")
R
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패키지 다운로드
$ wget http://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/absolute/ABSOLUTE_1.0.6.tar.gz
Shell
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패키지 설치
$ R CMD INSTALL ABSOLUTE
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확인
# in R
library(ABSOLUTE)
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예시 데이터 다운로드
$ wget ftp://ftp.broadinstitute.org/pub/genepattern/example_files/HAPSEG_1.1.1/paper_example.zip
Shell
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실행
ABSOLUTE 돌리기
RunAbsolute(
seg.dat.fn, # A filename pointing to the input.
sigma.p, # Provisional value of excess sample level variance for mode search
max.sigma.h, # Maximum value of excess sample level variance
min.ploidy, # Minimum ploidy value to consider. Solution implying lower ploidy values will be discarded.
max.ploidy, # Maximum ploidy value to consider. Solution implying greater ploidy values will be discarded.
primary.disease, # Primary disease of the sample
platform, # The chip type used, supported values are currently 'SNP_250K_STY', 'SNP_6.0', and 'Illumina_WES'
sample.name, # The name of the sample, included in output plots.
results.dir, # A directory path to place results. If the directory doesn't already exist, it will be created.
max.as.seg.count, # Maximum number of allelic segments. Samples with a higher segment count will be flagged as 'failed'.
max.non.clonal, # Maximum genome fraction that may be modeled as non-clonal (subclonal SCNA). Solutions implying greater values will be discarded.
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.
copy_num_type, # The copy number type to assess, can be one of 'allelic' or 'total'. Currently allelic must be used for HAPSEG based inputs and total for segmentation file based inputs.
maf.fn=NULL, # If available, a filename pointing to a mutation annotation format (MAF) file. This specifies the data for somatic point mutations to be used by ABSOLUTE.
min.mut.af=NULL, # If specified, a minimum mutation allelic fraction. Mutations with lower allelic fractions will be filtered out before analysis. Note that if maf.fn is specified, min.mut.af must also be specified.
output.fn.base=NULL, # If specified, provides a base filename for all output files. The default value is the array.name field in the object pointed to by seg.dat.fn or sample.name if this is not available.
verbose=FALSE # If you would like verbose output, supply this argument as being TRUE.
)
R
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CreateReviewObject
CreateReviewObject(
obj.name, # {sample}_summary
absolute.files, # {sample}.ABSOLUTE.RData
results.dir, # Result directory
"allelic", # or "total"
verbose=TRUE
)
Python
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ExtractReviewedResults
데이터 준비
Input 형태
파라미터 선정
•
sigma.p = 0.01
•
max.sigma.h = 0.02
•
min.ploidy = 0.95, max.ploidy = 10, max.as.seg.count = 1500, max.non.clonal = 0, max.neg.genome = 0
