getGeneExp(DEGseq)
getGeneExp()所属R语言包：DEGseq
getGeneExp: Count the number of reads and calculate the RPKM for each gene
getGeneExp：计数读取的数量，并计算出每个基因的RPKM
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function is used to count the number of reads and calculate the RPKM for each gene. It takes uniquely mapped reads from RNA-seq data for a sample with a gene annotation file as input. So users should map the reads (obtained from sequencing library of the sample) to the corresponding genome in advance.
此函数用于计算读取的数量，并计算出每个基因的RPKM。它采用独特的映射从基因注释文件作为输入样本的RNA-seq的数据读取。因此，用户应该映射读取测序样本库获得相应的基因组提前。
用法----------Usage----------
getGeneExp(mapResultBatch, fileFormat="bed", readLength=32, strandInfo=FALSE,
refFlat, output=paste(mapResultBatch[1],".exp",sep=""), min.overlapPercent=1)
参数----------Arguments----------
参数：mapResultBatch
vector containing uniquely mapping result files for a sample. <br> Note: The sample can have multiple technical replicates.
向量的独特的映射样本结果文件。参考注：样品可以有多个技术复制。
参数：fileFormat
file format: "bed" or "eland". <br> example of "bed" format: chr12 7 38 readID 2 + <br> example of "eland" format: readID chr12.fa 7 U2 F <br> Note: The field separator character is TAB. And the files must follow the format as one of the examples.
文件格式："bed"或"eland"。 "bed"格式：chr12 7 38 readID 2 +参考注：字段分隔符是"eland"readID chr12.fa 7 U2 FTAB格式参考范例的参考例子。和文件必须按照格式，作为一个例子。
参数：readLength
the length of the reads (only used if fileFormat="eland").
如果fileFormat="eland"读取长度（只用）。
参数：strandInfo
whether the strand information was retained during the cloning of the cDNAs.
是否被保留在克隆的cDNA链信息。
"TRUE" : retained,
"TRUE" ：保留，
"FALSE": not retained.
"FALSE"：不保留。
参数：refFlat
gene annotation file in UCSC refFlat format. <br> See http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat.
基因UCSC的refFlat格式的注释文件。参考见http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html＃RefFlat。
参数：output
the output file.
输出文件。
参数：min.overlapPercent
the minimum percentage of the overlapping length for a read and an exon over the length of the read itself, for counting this read from the exon. should be <=1. <br> 0: at least 1 bp overlap between a read and an exon.
搭接长度的最低比例为只读和一个外显子的长度，阅读本身，从外显子读计数。应该是<= 1。参考0：至少1BP只读和一个外显子之间的重叠。
注意----------Note----------
This function sums up the numbers of reads coming from all exons of a specific gene (according to the known gene annotation) as the gene expression value. The exons may include the 5'-UTR, protein coding region, and 3'-UTR of a gene. All introns are ignored for a gene for the sequenced reads are from the spliced transcript library. If a read falls in an exon (usually, a read is shorter than an exon), the read count for this exon plus 1. If a read is crossing the boundary of an exon, users can tune the parameter min.overlapPercent, which is the minimum percentage of the overlapping length for a read and an exon over the length of the read itself, for counting this read from the exon. The method use the union of all possible exons for calculating the length for each gene.
此功能总结了从一个特定的基因，基因表达值（根据已知的基因注释）的所有外显子的未来读取的数字。外显子可能包括5-UTR区，蛋白质编码区域，和3-UTR的基因。所有内含子被忽略了基因测序读是从拼接成绩单库。如果读落在一个外显子（通常情况下，一读就是短于外显子），读此外显子加1计数。如果读取一个外显子越过边界，用户可以调整参数min.overlapPercent，这是一个只读的重叠长度为最低百分比和外显子的长度超过了阅读本身，从这个只读计数外显子。使用该方法计算每一个基因的长度一切可能的外显子的工会。
参考文献----------References----------
参见----------See Also----------
DEGexp, DEGseq, readGeneExp, kidneyChr21.bed, liverChr21.bed, refFlatChr21.
DEGexp，DEGseq，readGeneExp，kidneyChr21.bed，liverChr21.bed，refFlatChr21。
举例----------Examples----------
kidneyR1L1 <- system.file("extdata", "kidneyChr21.bed.txt", package="DEGseq")
refFlat <- system.file("extdata", "refFlatChr21.txt", package="DEGseq")
mapResultBatch <- list(kidneyR1L1)
output <- file.path(tempdir(), "kidneyChr21.bed.exp")
exp <- getGeneExp(mapResultBatch, refFlat=refFlat, output=output)
write.table(exp[30:35,], row.names=FALSE)
cat("output: ", output, "\n")
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。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 16:26:39
