R语言 TEQC包 TEQCreport()函数中文帮助文档(中英文对照)

loveR

TEQCreport(TEQC)
TEQCreport()所属R语言包：TEQC

                                        Creates an html report
                                         创建一个HTML报告

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Creates an automated html report for the complete TEQC analysis of one sample
创建一个完整的一个样本TEQC分析自动化的HTML报告


用法----------Usage----------


TEQCreport(sampleName = "", targetsName = "", referenceName = "", destDir = "TEQCreport",
            reads = get.reads(), targets = get.targets(), Offset = 0, pairedend = FALSE, genome = c(NA, "hg19", "hg18"),
            genomesize, CovUniformityPlot = FALSE, CovTargetLengthPlot = FALSE, CovGCPlot = FALSE,
            duplicatesPlot = FALSE, baits = get.baits(), WigFiles = FALSE, saveWorkspace = FALSE)



参数----------Arguments----------

参数：sampleName
descriptive sample name; will be written on top of the html report
HTML报告的顶部将被写入描述样品的名称;


参数：targetsName
descriptive name of the captured target; will be written on top of the html report
将被写入HTML报告上捕获目标的描述性名称;


参数：referenceName
descriptive name of the reference genome the reads were aligned against; will be written on top of the html report
将被写入HTML报告上读取一致反对的参考基因组的描述性名称;


参数：destDir
directory where results and html documents shall be saved
结果和HTML文件，应保存的目录


参数：reads
RangedData table containing positions of sequenced reads, or call to get.reads to read in positions from a bed or BAM file
RangedData表包含的测序读，或致电get.reads在床或BAM文件位置读取的位置


参数：targets
RangedData table containing positions of target regions, or call to get.targets to read in positions from a bed file
RangedData表，其中包含目标区域的位置，或致电get.targets阅读从床上文件的位置


参数：Offset
integer; add Offset bases on both sides to targeted regions and potentially collapse resulting overlapping target regions
整数;加上Offset双方针对区域的碱基和潜在的崩溃导致重叠的目标区域


参数：pairedend
if TRUE, data will be considered to be paired-end data, i.e. reads will be "merged" to read pairs, and chromosome bar plot, specificity, enrichment and duplicate analysis (if selected) will be based on read pairs rather than on single reads
TRUE如果，数据将被认为是配对末端数据，即读取将“合并”阅读对染色体条形图，特异性，富集和重复分析（如果选择）将读对，而不是单一的读取


参数：genome
genome version targets were designed and reads aligned to. For the given options the total genome size is set automatically. For other genomes or versions, leave this option empty ('NA') and specify the genome size with option 'genomesize'
基因组版本的目标是设计和读取对齐。对于给定的选项全基因组的大小自动设置。其他基因或版本，离开这个选项为空（“不适用”），并指定选项“genomesize的基因组大小


参数：genomesize
integer: specify the total genome size manually. If 'genomesize' is given, option 'genome' will be ignored.
整数：手动指定的总基因组大小。如果genomesize“，选项基因将被忽略。


参数：CovUniformityPlot
if TRUE, a coverage uniformity plot is created, see coverage.uniformity
如果TRUE，创建一个覆盖均匀图，看到coverage.uniformity


参数：CovTargetLengthPlot
if TRUE, coverage vs target length plots are created, see coverage.targetlength.plot  
如果TRUE，覆盖面与目标长度图被创建时，看到coverage.targetlength.plot


参数：CovGCPlot
if TRUE, a coverage vs GC content plot is created, see coverage.GC
如果TRUE，建立覆盖与GC含量图，看到coverage.GC


参数：duplicatesPlot
if TRUE, a duplicates barplot is created, see duplicates.barplot
如果TRUE1重复barplot，创建，看到duplicates.barplot


参数：baits
A RangedData table holding the hybridization probe ("bait") positions and sequences, or call to get.baits to read in positions from a bed file. Only needed if CovGCPlot = TRUE.
一个RangedData表（“诱饵”）持有的杂交探针的位置和顺序，或致电get.baits阅读从床上文件的位置。只需如果CovGCPlot = TRUE。


参数：WigFiles
if TRUE, wiggle files with per-base coverage are created for each chromosome
如果TRUE，每个碱基的覆盖面摆动的文件创建为每个染色体


参数：saveWorkspace
if TRUE, an R workspace with objects reads, targets and output of coverage.target and reads2pairs (in case pairedend = TRUE) are saved in destDir to be available for further analyses
如果TRUE，对象ŕ工作区reads，targets和输出coverage.target和reads2pairs（万一pairedend = TRUE）保存在 destDir可作进一步分析


Details

详情----------Details----------

TEQC analysis is preformed and files for an html report are created in destDir. The report can be viewed by opening destDir/index.html in a web browser. Images are saved in destDir/image. Wiggle files (in case WigFiles = TRUE) are saved in destDir/wiggle. The table with coverage values per target and the R workspace containing R objects for potential further analysis (in case saveWorkspace = TRUE)
TEQC分析预制，并在destDir创建一个HTML报告文件。该报告可以被视为开放destDir/在浏览器中的index.html。图像将被保存在destDir/图像。摆动文件（的情况下WigFiles = TRUE）destDir/摆动保存。覆盖值每的目标和潜在的进一步分析含有R对象的R工作区的表（saveWorkspace = TRUE）


值----------Value----------

The function is invoked for its side effect
其副作用的函数被调用


作者（S）----------Author(s)----------


Manuela Hummel <a href="mailto:manuela.hummel@crg.es">manuela.hummel@crg.es</a>



参考文献----------References----------

target capture experiments. Bioinformatics 2011; doi: 10.1093/bioinformatics/btr122

参见----------See Also----------

get.reads, get.targets, fraction.target, fraction.reads.target, coverage.target, readsPerTarget, reads2pairs, covered.k, coverage.hist, coverage.uniformity, coverage.targetlength.plot, coverage.GC, get.baits,
get.reads，get.targets，fraction.target，fraction.reads.target，coverage.target，readsPerTarget，reads2pairs，covered.k，coverage.hist，coverage.uniformity，coverage.targetlength.plot，coverage.GC，get.baits


举例----------Examples----------


## get reads and targets files[＃获得读取目标文件]
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")

## create report[＃创建报告]
## Not run: [＃无法运行：]
TEQCreport(sampleName="Test Sample", targetsName="Human Exome", referenceName="Human Genome",
          destDir="report", reads=get.reads(readsfile, skip=0, idcol=4),
          targets=get.targets(targetsfile, skip=0), genome="hg19")
## End(Not run)[＃结束（不运行）]

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。