readVcf(VariantAnnotation)
readVcf()所属R语言包：VariantAnnotation
Read VCF (variant call format) files into a SummarizedExperiment object
VCF的（变异调用格式）文件阅读成SummarizedExperiment对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Read VCF files into a SummarizedExperiment object
vcf文件阅读成SummarizedExperiment对象
用法----------Usage----------
## S4 method for signature 'character,ANY'
readVcf(file, ..., param)
## S4 method for signature 'character,missing'
readVcf(file, ..., param)
## S4 method for signature 'TabixFile,GRanges'
readVcf(file, ..., param)
## S4 method for signature 'TabixFile,RangedData'
readVcf(file, ..., param)
## S4 method for signature 'TabixFile,RangesList'
readVcf(file, ..., param)
## S4 method for signature 'TabixFile,ScanVcfParam'
readVcf(file, ..., param)
## S4 method for signature 'TabixFile,missing'
readVcf(file, ..., param)
参数----------Arguments----------
参数：file
The character() file name(s) of the VCF file to be processed, or an instance of class TabixFile.
VCF文件的文件名的字符（）（S）进行处理，或TabixFile类的一个实例。
参数：param
A instance of GRanges, RangedData, RangesList, or ScanVcfParam providing the sequence names and regions to be parsed.
GRanges，RangedData，RangesList或ScanVcfParam提供的序列名称和区域的实例进行解析。
参数：...
Additional arguments, passed to methods.
额外的参数，传递给方法。
Details
详情----------Details----------
readVcf imports records from a VCF file into a SummarizedExperiment object. The param argument can be used to select a subset of records when reading from compressed (bgzip) VCF files.
readVcfSummarizedExperiment对象从VCF文件的进口记录。 param参数可用于选择从阅读压缩（bgzip）的vcf文件时记录的一个子集。
The function calls Rsamtools scanVcf, the details of which can be found with ?scanVcf.
函数调用RsamtoolsscanVcf，其中的细节，可以用?scanVcf。
值----------Value----------
The object returned is a SummarizedExperiment. See the help page for SummarizedExperiment for complete details of the class structure.
返回的对象是一个SummarizedExperiment。 SummarizedExperiment类结构的完整的详细信息，请参阅帮助页面。
The rowData slot contains a GRanges instance with metadata columns of QUAL (phred-scaled quality for the assertion made in ALT), FILTER (pass if position passed all filters), INFO (additional information), REF (reference base(s)), and ALT (alternate non-reference alleles called on at least one of the samples) fields in the VCF file. The row names of the GRanges object are the ID values from the VCF file if they exist. See references for complete details of the VCF file format. The ranges in the rowData reflect the range of the REF alleles.
rowData槽包含元数据列QUAL（PHRED规模的质量，在ALT断言），过滤GRanges的位置，如果通过所有过滤器的实例（通），信息（附加信息），楼盘（参考基准（S））和ALT（替代非参考至少一个样品称为等位基因）VCF文件中的字段。 GRanges对象的行名是从VCF文件的ID值，如果它们存在。 VCF文件格式的完整细节，请参阅参考。在范围rowData反映楼盘等位基因的范围。
The assays slot is a list the same length as the number of fields in the FORMAT column of the VCF file. Each list element is a matrix of data from the GENO field where there is a row for each variant and a column for each sample.
assays槽是一个列表的长度相同领域中的VCF文件格式列。每个列表元素是从那里是一个对每个变种的行和列每个样品的基因型领域的数据矩阵。
The colData slot contains a DataFrame describing the samples. If present, the sample names (i.e., the names following GENO in the VCF file), become the row names.
colData槽包含一个DataFrame描述样品。如果存在，样品名称（即基因型后，在VCF文件的名称），成为该行的名称。
The exptData slot contains a SimpleList with the VCF file header information.
exptData槽包含一个VCF文件头信息SimpleList。
作者（S）----------Author(s)----------
Valerie Obenchain <vobencha@fhcrc.org>
参考文献----------References----------
specification.
information on the portion of the specification implemented by <code>bcftools</code>.
<code>samtools</code>.
参见----------See Also----------
indexTabix TabixFile scanTabix scanBcf
indexTabixTabixFilescanTabixscanBcf
举例----------Examples----------
## read all records of VCF into a SummarizedExperiment[＃读取SummarizedExperiment成VCF的所有记录]
vcfFile <- system.file("extdata", "ex1.vcf", package="VariantAnnotation")
vcf <- readVcf(vcfFile)
names(assays(vcf))
## compress on the fly and read a subset of data[＃压缩和读取数据的一个子集的飞]
rngs <- GRanges(seqnames="1", ranges=IRanges(start=0, end=100000))
compressVcf <- bgzip(vcfFile, tempfile())
idx <- indexTabix(compressVcf, "vcf")
tab <- TabixFile(compressVcf, idx)
vcf <- readVcf(tab, param=rngs)
## VCF header information [＃VCF的头信息]
vcf
exptData(vcf)[["HEADER"]]
exptData(vcf)[["HEADER"]][["META"]]
## the 8 required VCF fields are parsed into the rowData slot[＃8所需的VCF的领域被解析成rowData插槽]
exptData(vcf)[["HEADER"]][["FILTER"]]
exptData(vcf)[["HEADER"]][["INFO"]]
rowData(vcf)
## genotype data described in FORMAT are parsed into the assays slot [＃基因型格式的数据解析成检测槽]
exptData(vcf)[["HEADER"]][["FORMAT"]]
assays(vcf)
head(assays(vcf)$GT)
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
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发表于 2012-2-26 15:57:30
