Harshlight(Harshlight)
Harshlight()所属R语言包：Harshlight
a blemish detection program for microarray chips: extended, diffuse, and compact defects
为微阵列芯片缺陷检测方案：扩展，弥漫，紧凑的缺陷
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Harshlight automatically detects and masks blemishes in microarray chips of class AffyBatch
harshlight自动检测和口罩类AffyBatch微阵列芯片瑕疵
用法----------Usage----------
Harshlight(affy.object, my.ErrorImage = NULL, extended.radius = 10,
compact.quant.bright = 0.025, compact.quant.dark = 0.025,
compact.size.limit = 15, compact.connect = 8, compact.pval = 0.01,
diffuse.bright = 40, diffuse.dark = 35, diffuse.pval = 0.001,
diffuse.connect = 8, diffuse.radius = 10,
diffuse.size.limit = (3*3.14*(diffuse.radius**2)),
percent.contiguity = 50, report.name = 'R.report.ps', na.sub = FALSE,
interpolate = TRUE, diffuse.close = TRUE)
参数----------Arguments----------
参数：affy.object
An AffyBatch object containing two or more chips.
一个AffyBatch对象包含两个或更多的筹码。
参数：my.ErrorImage
A batch of ErrorImages obtained through other programs. The error images must be in a matrix format, in which the first index represents each cell in the matrix and the second index represents the chip number. By default, the program calculates the error images for the batch of chips affy.object as described in Suarez-Farinas M et al., BMC Bioinformatics - 2005. If a batch of error images is provided, the affy.object is also required.
通过其他程序获得的一批ErrorImages。错误的图像，必须是在一个矩阵格式，其中第一个索引矩阵中的每个单元，第二个指数所代表的芯片数量。默认情况下，程序计算错误苏亚雷斯-Farinas M等，BMC的生物信息学为芯片affy.object的一批图像 - 2005年。如果提供了一批错误的图像，affy.object也是必需的。
参数：extended.radius
Radius of the median kernel used to identify extended defects on the chip.
用于识别芯片的扩展缺陷中位数的内核半径。
参数：compact.quant.bright, compact.quant.dark
Quantiles of the Error Image used to declare outliers. Values bigger than the '(1 - compact.quant.bright)' percentile are bright outliers, while values smaller than the 'compact.quant.dark' percentile are dark outliers. The two quantiles are used to detect compact defects. Set it to 0 to turn compact defect detection off.
位数的用于声明离群的错误图片。更大的百分比“（1 - compact.quant.bright）值是明亮的离群值，而值小于”compact.quant.dark“百分黑暗离群。两位数是用于检测紧凑缺陷。它设置为0，把紧凑的缺陷检测。
参数：compact.size.limit, diffuse.size.limit
Minimum size for clusters to be considered defects. If 0, all the clusters identified will be considered defects, if their size is significantly bigger than the one expected by chance (see also compact.pval).
聚类的最小尺寸被视为缺陷。如果为0，所有的聚类确定将被视为缺陷，如果他们的规模比由机会（也compact.pval）预计一大显着。
参数：compact.connect, diffuse.connect
Defines the neighbourhood of a pixel, used to connect outliers into clusters. If 4, the neighbourhood contains the pixels that are adjacent of a pixel of reference, on the vertical or horizontal axis. If 8, the neighbourhood contains all the 8 pixels sorrounding the pixel of reference. If a connectivity of 4 is used, clusters that are connected only through an edge will be considered as separate clusters. In this case, the single clusters could be eliminated because their size does not exceed compact.size.limit or diffuse.size.limit. Therefore, we suggest to use a connectivity of 8.
定义附近的一个像素，用于连接到聚类离群。如果4，邻里包含相邻的水平或垂直轴的参考像素，像素。如果是8，邻里包含所有的8个像素sorrounding参考像素。如果使用了4连通，只有通过边缘连接的聚类将被视为独立的聚类。在这种情况下，单簇可能被淘汰，因为它们的大小不超过compact.size.limit或diffuse.size.limit。因此，我们建议使用8连通。
参数：compact.pval
Threshold for compact defect size. This is the maximum probability accepted to find a cluster of the same size by chance. If 1, a cluster is considered a compact defect if it is bigger than the value of compact.size.limit.
紧凑型缺损大小的阈值。这是接受的最大概率，找到一个偶然的大小相同的聚类。如果为1，聚类被认为是一个紧凑的缺陷如果是大于价值compact.size.limit的。
参数：diffuse.bright, diffuse.dark
Percentage of increase (bright) or decrease (dark) of the intensity value of a pixel compared to the expected intensity. Used to declare outliers to detect diffuse defects. The option to detect diffuse defects is turned off if the value is set to 0.
增加的百分比（亮）或减少一个像素的亮度值（暗），比预期的强度。用来声明离群检测弥漫性缺陷。检测弥漫性缺陷的选项是关闭的，如果该值设置为0。
参数：diffuse.radius
Radius of the mask used to identify diffuse defects on the chip. Inside this mask the binomial test is performed.
遮罩半径用于识别芯片上弥漫缺陷。这里面面具二项式测试。
参数：diffuse.pval
Significance for the binomial test during diffuse defects' detection.
二项式测试期间弥漫性缺陷检测的意义。
参数：percent.contiguity
Minimum percentage of area density for defects to be considered compact. If 0, every compact defect found will be eliminated before searching for diffuse defects. Though possible, avoid using less than 20; otherwise diffuse defects might not be identified properly.
缺陷区域密度最低的百分比被视为紧凑。如果为0，每一个紧凑发现的缺陷会被淘汰之前，寻找弥漫性缺陷。虽然尽量避免使用小于20;否则漫缺陷可能无法确定正确的。
参数：report.name
Name of the PostScript file in which to save the final report. If report.name is set to ”, no report will be written.
PostScript文件名，在其中保存的最后报告。 ，如果report.name设置为“，没有报告将被写入。
参数：na.sub
If TRUE, the intensity values of the input affyBatch that are affected by defects will be changed in NA. If FALSE, the values will be substituted with the median of the intensity values of the other chips.
如果是TRUE，缺陷影响的输入affyBatch的强度值将在NA改变。如果为FALSE，该值将被替换为其他芯片的强度值的中位数。
参数：interpolate
This option is only used if the value of compact.quant.bright or compact.quant.dark is not among those tabulated (density of outliers = 0.01, 0.02, 0.05, 0.10, 0.20, 0.25, 0.30, 0.40; chip size = 534x534, 640x640, 712x712). If TRUE, the cluster size distribution under the null hypothesis of spatially randomly distributed outliers is derived from simulated values through interpolation. If FALSE, the distribution is simulated for the input value of density of outliers (compact.quant.bright/compact.quant.dark) and the specific chip size. The program runs 100.000 simulations by default.
此选项仅用于值如果compact.quant.bright或compact.quant.dark的是不属于表（离群密度= 0.01，0.02，0.05，0.10，0.20，0.25，0.30，0.40;芯片尺寸= 534x534 ，640x640，712x712）。如果是TRUE，零假设下的空间随机分布的离群簇大小分布是来自模拟值通过插值。如果为FALSE，分布是离群密度输入值（compact.quant.bright / compact.quant.dark）和特定的芯片尺寸的模拟。默认情况下，程序运行100.000模拟。
参数：diffuse.close
If TRUE, the whole area in which the diffuse defects are included is considered as a defect. If FALSE, only the outliers inside the area are considered defects.
如果为TRUE，在其中弥漫性缺陷包括整个区域被视为缺陷。如果为FALSE，只有在禁区内的离群，被认为是缺陷。
值----------Value----------
参数：AffyBatch object
The input AffyBatch object, whose intensity values corresponding to defected areas are substituted either by NA or by the median of the chip's values (depending on na.sub).
在的输入AffyBatch对象，其强度值对应于缺损区取代NA或芯片的价值观（取决于对na.sub）的中位数。
参数：Report
For each AffyBatch analyzed, a report is written as a PostScript file (see also report.name).
对于每个AffyBatch分析，书面报告是为PostScript文件（也report.name）。
作者（S）----------Author(s)----------
Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkwosky, Marcelo O. Magnasco
<a href="mailto:mpellegri@rockefeller.edu">mpellegri@rockefeller.edu</a>
参考文献----------References----------
举例----------Examples----------
## To run the example, download the affybatch object example.rda[＃要运行的例子，下载的affybatch的对象example.rda]
## from the website http://asterion.rockefeller.edu/Harshlight/[＃网站http://asterion.rockefeller.edu/Harshlight/的]
## Not run: [＃无法运行：]
source("example.rda") ## this creates the object my.affybatch in your working environment[＃此创建您的工作环境中的对象my.affybatch]
library(Harshlight)
harsh <- Harshlight(affy.object = my.affybatch, report.name = 'example.ps') ## The file example.ps will appear in your working directory[＃的的文件example.ps将出现在你的工作目录]
## Calculate expression measures using MAS5[＃计算表达式措施使用MAS5]
mas.example <- mas5(my.affybatch)
mas.harsh <- mas5(harsh)
plot(log2(exprs(mas.example)),log2(exprs(mas.harsh)))
## 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 21:30:04
