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Last data update: 2014.03.03

R: Read data from macSynergyII format and clean for outliers.

readMacSynergyValues

R Documentation

Read data from macSynergyII format and clean for outliers.

Description

Read data from macSynergyII format and clean for outliers.

Usage

readMacSynergyValues(file, sheet, nrow = 41, wellRangesExcel,
  minThersholdForCVCal, minThersholdForCV)

Arguments

`file`	Name of file containing data.
`sheet`	Sheet number in a spread sheet workbook.
`nrow`	Number of rows in that sheet to be read.
`wellRangesExcel`	TRUE if input wells ranges are in excel format.
`minThersholdForCVCal`	CV threshold for data outliers.
`minThersholdForCV`	Threshold of survival values not used for CV calculations.

Value

Matrix of outlier removed data replicates.

Author(s)

Muhammad kashif

Examples

fl <- system.file("/raw/testData.xls", package="COMBIA")
sh <- 1
wellR <- list(c( "l3:l10","m3:m10","b3:k10",  "l13:l20","m13:m20","b13:k20",
           "l23:l30","m23:m30","b23:k30",  "l33:l40","m33:m40","b33:k40"))
minThersholdForCV <- 0.3
minThersholdForCVCal <- 0.1
rslt <- readMacSynergyValues(fl, sh, nrow=41, wellR,
minThersholdForCVCal, minThersholdForCV)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(COMBIA)
Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

The following object is masked from 'package:utils':

    object.size

The following object is masked from 'package:base':

    startsWith

Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: oro.nifti
oro.nifti 0.5.2
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/COMBIA/readMacSynergyValues.Rd_%03d_medium.png", width=480, height=480)
> ### Name: readMacSynergyValues
> ### Title: Read data from macSynergyII format and clean for outliers.
> ### Aliases: readMacSynergyValues
> 
> ### ** Examples
> 
> fl <- system.file("/raw/testData.xls", package="COMBIA")
> sh <- 1
> wellR <- list(c( "l3:l10","m3:m10","b3:k10",  "l13:l20","m13:m20","b13:k20",
+            "l23:l30","m23:m30","b23:k30",  "l33:l40","m33:m40","b33:k40"))
> minThersholdForCV <- 0.3
> minThersholdForCVCal <- 0.1
> rslt <- readMacSynergyValues(fl, sh, nrow=41, wellR,
+ minThersholdForCVCal, minThersholdForCV)
[1] "Ratio between empty and control 215.34756097561"
[1] "CV for control: 1 : 2.30698484671909"
[1] "Ratio between empty and control 216.431571815718"
[1] "CV for control: 2 : 3.97477131010254"
[1] "Ratio between empty and control 212.255570117955"
[1] "CV for control: 3 : 6.4008999376604"
[1] "Ratio between empty and control 191.453473132372"
[1] "CV for control: 4 : 5.87005801002331"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>