plotFragLength(ggbio)
plotFragLength()所属R语言包：ggbio
Plot estimated fragment length for paired-end RNA-seq data
图配对末端的RNA-seq的数据估计片段长度
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plot estimated fragment length for paired-end RNA-seq data against single reduced data model.
图片段长度为RNA-seq的配对末端对单减少数据模型的数据估计。
用法----------Usage----------
## S4 method for signature 'character,GRanges'
plotFragLength(data, model,
gap.ratio = 0.0025,
geom = c("segment", "point", "line"),
type = c("normal", "cut"),
heights = c(400, 100),
annotation = TRUE)
参数----------Arguments----------
参数：data
A character indicate the bam file.
字符显示的BAM文件。
参数：model
A reduced model to compute estimated fragment length. please see details.
一个简化模型来计算，估计片段长度。请参阅详情。
参数：gap.ratio
When type is set to "cut", it will provide a compact view, which cut the common gaps in a certain ratio.
当类型设置为“腰斩”，它会提供一个紧凑的观点，这削减一定比例共同的差距。
参数：geom
One or all three geoms could be drawn at the same time. y value of "point" and "line" indicate the estimated fragment length. and if geom is set to "segment", the segment is from the left most position to paired right most position, should be equal to "isize".
在同一时间，可以得出一个或所有三个geoms。 “点”和“行”的Y值表示估计片段长度。 GEOM如果被设置为“段”，段是从最左边的位置，配对正确的。大部分的位置，应该是等于“isize”。
参数：type
"normal" return a uncut view, loose but the coordinate is true genomic coordinates. "cut" cut the view in a compact way.
“正常的”返回一个完整无缺的观点，宽松，但坐标是真正的基因坐标。 “切”切在一个紧凑的方式。
参数：heights
Numeric vector indicate the heights of tracks.
数字矢量显示的轨道高度。
参数：annotation
A logical value. TRUE shows model, and FALSE shows only fragment length with labels.
一个逻辑值。真正的表演模式，和FALSE表演片段长度与标签。
Details
详情----------Details----------
We use a easy way to define this estimated fragment length, we collect all paired reads and model, reduce model first, then find common gaps, remove common gaps between paired-end reads, and compute the new estimated fragment length.
我们用一个简单的方法来定义这种估计的片段长度，我们收集的所有配对读取和模型，减少模型，然后找到共同的差距，除去常见的差距之间的配对末端读取，并计算新的估计片段长度。
值----------Value----------
A ggplot object when annotation = FALSE and a frame grob if annotation = TRUE
一个ggplot对象时，如果annotation = FALSE帧GROB annotation = TRUE
作者（S）----------Author(s)----------
Tengfei Yin
举例----------Examples----------
## Not run: [＃无法运行：]
data(genesymbol)
bamfile <- system.file("extdata", "SRR027894subRBM17.bam", package="biovizBase")
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- Hsapiens_UCSC_hg19_knownGene_TxDb
model <- exonsBy(txdb, by = "tx")
model.new <- subsetByOverlaps(model, genesymbol["RBM17"])
exons.rbm17 <- subsetByOverlaps(exons(txdb), genesymbol["RBM17"])
exons.new <- reduce(exons.rbm17)
plotFragLength(bamfile, exons.new, geom = "line")
plotFragLength(bamfile, exons.new, geom = c("point","segment"))
plotFragLength(bamfile, exons.new, geom = c("point","segment"), annotation = FALSE)
plotFragLength(bamfile, exons.new, geom = c("point","segment"), type = "cut",
gap.ratio = 0.001)
## 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。
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发表于 2012-2-25 19:44:20
