spotseg(spotSegmentation)
spotseg()所属R语言包：spotSegmentation
Microarray Spot Segmentation
芯片现货分割
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Microarray spot segmentation via model-based clustering.
通过基于模型的聚类的微阵列点分割。
用法----------Usage----------
参数----------Arguments----------
参数：chan1
matrix of pixel intensities from the first channel.
从第一通道的像素强度的矩阵。
参数：chan2
matrix of pixel intensities from the second channel.
从第二通道的像素强度的矩阵。
参数：rowcut
row delimiters for the spots. Entries are the starting row location in the close of each spot, with the last entry being one pixel beyond the border of the last spot. For example, from the output of spotgrid.
斑点的行分隔符。条目是在每场结束行位置的最后一个条目，超越边界的最后一个景点的一个像素。例如，从输出spotgrid。
参数：colcut
column delimiters for the spots. Entries are the starting column location in the close of each spot, with the last entry being one pixel beyond the border of the last spot. For example, from the output of spotgrid.
斑点的列分隔符。条目是在每场结束的最后一个条目，超越边界的最后一个景点的一个像素的起始列位置。例如，从输出spotgrid。
参数：R
rows over which the spots are to be segmented. The default is to segment spots in all rows.
该点分割的行。默认是在所有行的段点。
参数：C
columns over which the spots are to be segmented. The default is to segment spots in all columns.
列该点分割。默认是在所有列的段点。
参数：threshold
connected components of size smaller than threshold are ignored. Default: threshold=100.
连接组件的大小比threshold小被忽略。默认：threshold=100。
参数：hc
logical variable indicating whether or not EM should be initialized by hierarchical clustering or quantiles in model-based clustering. The default is to use quantiles hc = FALSE, which is more efficient both in terms of speed and memory usage.
逻辑变量表示EM是否应在基于模型的聚类层次聚类或位数初始化。默认是使用位数hc = FALSE，这是更有效的，无论是在速度和内存使用方面。
参数：show
logical variable indicating whether or not to display the segmentation of each individual spot as it is processed. The default is not to display the spots show = FALSE.
逻辑变量表示是否显示分割处理，因为它是每一个人的位置。默认是不显示点show = FALSE。
Details
详情----------Details----------
There are plot and summary methods that can
有plot和summary方法可以
值----------Value----------
An array of the same dimensions as the image in which the pixels are labeled according to their group within the
图像像素标记内，根据他们的小组尺寸相同的数组
注意----------Note----------
The mclust package is requiredfor clustering.
mclust包是requiredfor聚类。
参考文献----------References----------
Robust model-based segmentation of microarray images,\ Technical Report No.~473, Department of Statistics, University of Washington, January 2005.
参见----------See Also----------
summary.spotseg, plot.spotseg,
summary.spotseg，plot.spotseg
举例----------Examples----------
data(spotSegTest)
# columns of spotSegTest:[对spotSegTest的列：]
# 1 intensities from the Cy3 (green) channel[1，从强度Cy3标记（绿色）通道]
# 2 intensities from the Cy5 (red) channel[2，从强度的Cy5的（红色）通道]
dataTransformation <- function(x) (256*256-1-x)^2*4.71542407E-05
chan1 <- matrix(dataTransformation(spotSegTest[,1]), 144, 199)
chan2 <- matrix(dataTransformation(spotSegTest[,2]), 144, 199)
Grid <- spotgrid( chan1, chan2, rows = 4, cols = 6, show = TRUE)
library(mclust)
Seg <- spotseg( chan1, chan2, Grid$rowcut, Grid$colcut)
plot(Seg)
spotSummary <- summary(Seg)
spot11 <- spotseg( chan1, chan2, Grid$rowcut, Grid$colcut,
R = 1, C = 1, show = TRUE)
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。
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发表于 2012-2-26 15:00:41
