estimates: estimates
In CONFESS: Cell OrderiNg by FluorEScence Signal
Description
Usage
Format
Value
Description
Example output of the SpotEstimator function
Usage
1
data("estimates")
Format
The format is:
List of 6
$ SpotResults :'data.frame': 14 obs. of 14 variables:
..$ SampleID : chr [1:14] "1772-062-248_A01" "1772-062-248_A02" "1772-062-248_A03" "1772-062-248_A04" ...
..$ X : num [1:14] 259 491 262 261 261 258 259 189 498 194 ...
..$ Y : num [1:14] 367 219 368 369 335 367 336 278 20 284 ...
..$ Size : num [1:14] 31 49 19 152 141 43 59 15 49 32 ...
..$ Estimation.Type: chr [1:14] "Both.Channels" "Both.Channels" "One.Channel" "One.Channel" ...
..$ fore_Green : num [1:14] 48.4 36 26.2 45.7 32.6 ...
..$ back_Green : num [1:14] 17.2 17.3 16.6 16.9 17.1 ...
..$ fore_Red : num [1:14] 219.1 27.6 86.5 18.4 48 ...
..$ back_Red : num [1:14] 17.5 18.6 17.5 18.1 18 ...
..$ Green.StN : num [1:14] 1.442 1.01 0.626 1.389 0.889 ...
..$ Green.Pvalue : num [1:14] 6.03e-07 1.08e-03 5.55e-02 5.16e-27 4.57e-23 ...
..$ Red.StN : num [1:14] 3.5689 0.5455 2.2422 0.0256 1.3664 ...
..$ Red.Pvalue : num [1:14] 6.16e-07 2.68e-01 7.13e-05 1.00 3.33e-25 ...
..$ Other.Spots : chr [1:14] "0" "0" "X = 30, Y = 204 (Green) | X = 262, Y = 368 (Red)" "0" ...
$ Outlier.Estimates:List of 14
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A01"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A02"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A03"
.. ..$ centerR: num [1:2] 263 370
.. ..$ centerG: num [1:2] 263 370
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A04"
.. ..$ centerR: num [1:2] 265 370
.. ..$ centerG: num [1:2] 265 370
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A05"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A06"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-062-248_A07"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A01"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A02"
.. ..$ centerR: num [1:2] 195 250
.. ..$ centerG: num [1:2] 195 250
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A03"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A04"
.. ..$ centerR: num [1:2] 191 281
.. ..$ centerG: num [1:2] 191 281
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A05"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A06"
.. ..$ centerR: num [1:2] 187 274
.. ..$ centerG: num [1:2] 187 274
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : chr "BF"
..$ :List of 6
.. ..$ sample : chr "1772-067-039_A07"
.. ..$ centerR: num [1:2] 0 0
.. ..$ centerG: num [1:2] 0 0
.. ..$ arR : NULL
.. ..$ arG : NULL
.. ..$ warn : NULL
$ Processed.Files :List of 6
..$ BF : chr [1:14] "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-062-248_A01_BF.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-062-248_A02_BF.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-062-248_A03_BF.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-062-248_A04_BF.txt" ...
..$ CH1 : chr [1:14] "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A01_Green.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A02_Green.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A03_Green.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A04_Green.txt" ...
..$ CH2 : chr [1:14] "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A01_Red.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A02_Red.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A03_Red.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A04_Red.txt" ...
..$ separator : chr "_"
..$ image.type: chr [1:3] "BF" "Green" "Red"
..$ dateIndex : chr "WedApr611:21:282016"
$ BFarea : num 7
$ image.type : chr [1:3] "BF" "Green" "Red"
$ dateIndex : chr "WedApr611:21:282016"
Value
example intermediates
CONFESS documentation built on Nov. 8, 2020, 6:05 p.m.
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Description Usage Format Value
Description
Example output of the SpotEstimator function
Usage
1 | data("estimates")
|
Format
The format is: List of 6 $ SpotResults :'data.frame': 14 obs. of 14 variables: ..$ SampleID : chr [1:14] "1772-062-248_A01" "1772-062-248_A02" "1772-062-248_A03" "1772-062-248_A04" ... ..$ X : num [1:14] 259 491 262 261 261 258 259 189 498 194 ... ..$ Y : num [1:14] 367 219 368 369 335 367 336 278 20 284 ... ..$ Size : num [1:14] 31 49 19 152 141 43 59 15 49 32 ... ..$ Estimation.Type: chr [1:14] "Both.Channels" "Both.Channels" "One.Channel" "One.Channel" ... ..$ fore_Green : num [1:14] 48.4 36 26.2 45.7 32.6 ... ..$ back_Green : num [1:14] 17.2 17.3 16.6 16.9 17.1 ... ..$ fore_Red : num [1:14] 219.1 27.6 86.5 18.4 48 ... ..$ back_Red : num [1:14] 17.5 18.6 17.5 18.1 18 ... ..$ Green.StN : num [1:14] 1.442 1.01 0.626 1.389 0.889 ... ..$ Green.Pvalue : num [1:14] 6.03e-07 1.08e-03 5.55e-02 5.16e-27 4.57e-23 ... ..$ Red.StN : num [1:14] 3.5689 0.5455 2.2422 0.0256 1.3664 ... ..$ Red.Pvalue : num [1:14] 6.16e-07 2.68e-01 7.13e-05 1.00 3.33e-25 ... ..$ Other.Spots : chr [1:14] "0" "0" "X = 30, Y = 204 (Green) | X = 262, Y = 368 (Red)" "0" ... $ Outlier.Estimates:List of 14 ..$ :List of 6 .. ..$ sample : chr "1772-062-248_A01" .. ..$ centerR: num [1:2] 0 0 .. ..$ centerG: num [1:2] 0 0 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : NULL ..$ :List of 6 .. ..$ sample : chr "1772-062-248_A02" .. ..$ centerR: num [1:2] 0 0 .. ..$ centerG: num [1:2] 0 0 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : NULL ..$ :List of 6 .. ..$ sample : chr "1772-062-248_A03" .. ..$ centerR: num [1:2] 263 370 .. ..$ centerG: num [1:2] 263 370 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : chr "BF" ..$ :List of 6 .. ..$ sample : chr "1772-062-248_A04" .. ..$ centerR: num [1:2] 265 370 .. ..$ centerG: num [1:2] 265 370 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : chr "BF" ..$ :List of 6 .. ..$ sample : chr "1772-062-248_A05" .. ..$ centerR: num [1:2] 0 0 .. ..$ centerG: num [1:2] 0 0 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : NULL ..$ :List of 6 .. ..$ sample : chr "1772-062-248_A06" .. ..$ centerR: num [1:2] 0 0 .. ..$ centerG: num [1:2] 0 0 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : NULL ..$ :List of 6 .. ..$ sample : chr "1772-062-248_A07" .. ..$ centerR: num [1:2] 0 0 .. ..$ centerG: num [1:2] 0 0 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : NULL ..$ :List of 6 .. ..$ sample : chr "1772-067-039_A01" .. ..$ centerR: num [1:2] 0 0 .. ..$ centerG: num [1:2] 0 0 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : NULL ..$ :List of 6 .. ..$ sample : chr "1772-067-039_A02" .. ..$ centerR: num [1:2] 195 250 .. ..$ centerG: num [1:2] 195 250 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : chr "BF" ..$ :List of 6 .. ..$ sample : chr "1772-067-039_A03" .. ..$ centerR: num [1:2] 0 0 .. ..$ centerG: num [1:2] 0 0 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : NULL ..$ :List of 6 .. ..$ sample : chr "1772-067-039_A04" .. ..$ centerR: num [1:2] 191 281 .. ..$ centerG: num [1:2] 191 281 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : chr "BF" ..$ :List of 6 .. ..$ sample : chr "1772-067-039_A05" .. ..$ centerR: num [1:2] 0 0 .. ..$ centerG: num [1:2] 0 0 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : NULL ..$ :List of 6 .. ..$ sample : chr "1772-067-039_A06" .. ..$ centerR: num [1:2] 187 274 .. ..$ centerG: num [1:2] 187 274 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : chr "BF" ..$ :List of 6 .. ..$ sample : chr "1772-067-039_A07" .. ..$ centerR: num [1:2] 0 0 .. ..$ centerG: num [1:2] 0 0 .. ..$ arR : NULL .. ..$ arG : NULL .. ..$ warn : NULL $ Processed.Files :List of 6 ..$ BF : chr [1:14] "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-062-248_A01_BF.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-062-248_A02_BF.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-062-248_A03_BF.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/BF/1772-062-248_A04_BF.txt" ... ..$ CH1 : chr [1:14] "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A01_Green.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A02_Green.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A03_Green.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A04_Green.txt" ... ..$ CH2 : chr [1:14] "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A01_Red.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A02_Red.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A03_Red.txt" "/home/diana/R/x86_64-pc-linux-gnu-library/3.2/CONFESSdata/extdata/CH/1772-062-248_A04_Red.txt" ... ..$ separator : chr "_" ..$ image.type: chr [1:3] "BF" "Green" "Red" ..$ dateIndex : chr "WedApr611:21:282016" $ BFarea : num 7 $ image.type : chr [1:3] "BF" "Green" "Red" $ dateIndex : chr "WedApr611:21:282016"
Value
example intermediates
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