1. PureCN
  2. R
  3. createCurationFile.R
Browse code

Version bump to make next stable 2.0; linting of some older code.

Markus Riester authored on 19/09/2021 18:58:19
Showing 1 changed files
R/createCurationFile.R
History View file @ 346ab89
... ... 
@@ -1,9 +1,9 @@
1 1 
 #' Create file to curate PureCN results
2 
-#'
2 
+#'
3 3 
 #' Function to create a CSV file that can be used to mark the correct solution
4 4 
 #' in the output of a \code{\link{runAbsoluteCN}} run.
5 
-#'
6 
-#'
5 
+#'
6 
+#'
7 7 
 #' @param file.rds Output of the \code{\link{runAbsoluteCN}} function,
8 8 
 #' serialized with \code{saveRDS}.
9 9 
 #' @param overwrite.uncurated Overwrite existing files unless flagged as
... ... 
@@ -15,48 +15,48 @@
15 15 
 #' @author Markus Riester
16 16 
 #' @seealso \code{\link{runAbsoluteCN}}
17 17 
 #' @examples
18 
-#'
18 
+#'
19 19 
 #' data(purecn.example.output)
20 20 
 #' file.rds <- "Sample1_PureCN.rds"
21 
-#' saveRDS(purecn.example.output, file=file.rds)
22 
-#' createCurationFile(file.rds)
23 
-#'
21 
+#' saveRDS(purecn.example.output, file = file.rds)
22 
+#' createCurationFile(file.rds)
23 
+#'
24 24 
 #' @export createCurationFile
25 25 
 #' @importFrom utils write.csv
26 
-createCurationFile <- function(file.rds, overwrite.uncurated = TRUE,
27 
-    overwrite.curated=FALSE) {
26 
+createCurationFile <- function(file.rds, overwrite.uncurated = TRUE,
27 
+                               overwrite.curated = FALSE) {
28 28 
     rds <- readRDS(file.rds)
29 29 
     res <- rds$results[[1]]
30 30 
     contamination <- res$SNV.posterior$posterior.contamination
31 31 
     contamination <- if (is.null(contamination)) 0 else contamination
32 32 
     d.f.curation <- data.frame(
33 
-        Sampleid=res$seg$ID[1],
34 
-        Purity=res$purity,
35 
-        Ploidy=res$ploidy,
36 
-        Sex=.getSexFromRds(rds),
37 
-        Contamination=contamination,
38 
-        Flagged=res$flag,
39 
-        Failed=FALSE,
40 
-        Curated=FALSE,
41 
-        Comment=res$flag_comment
33 
+        Sampleid = res$seg$ID[1],
34 
+        Purity = res$purity,
35 
+        Ploidy = res$ploidy,
36 
+        Sex = .getSexFromRds(rds),
37 
+        Contamination = contamination,
38 
+        Flagged = res$flag,
39 
+        Failed = FALSE,
40 
+        Curated = FALSE,
41 
+        Comment = res$flag_comment
42 42 
     )
43 43
44 
-    filename <- file.path(dirname(file.rds),
45 
-        paste(gsub(".rds$", "", basename(file.rds)), "csv", sep="."))
44 
+    filename <- file.path(dirname(file.rds),
45 
+        paste(gsub(".rds$", "", basename(file.rds)), "csv", sep = "."))
46 46
47 47 
     if (file.exists(filename)) {
48 
-        tmp <- read.csv(filename, as.is=TRUE)
48 
+        tmp <- read.csv(filename, as.is = TRUE)
49 49 
         if (tmp$Curated[1] && !overwrite.curated) {
50 
-            warning(filename,
50 
+            warning(filename,
51 51 
                 " already exists and seems to be edited.",
52 52 
                 " Will not overwrite it.")
53 53 
         } else if (!overwrite.uncurated) {
54 54 
             warning(filename, " already exists. Will not overwrite it.")
55 55 
         } else {
56 
-            write.csv(d.f.curation, file=filename, row.names=FALSE)
57 
-        }
56 
+            write.csv(d.f.curation, file = filename, row.names = FALSE)
57 
+        }
58 58 
     } else {
59 
-        write.csv(d.f.curation, file=filename, row.names=FALSE)
59 
+        write.csv(d.f.curation, file = filename, row.names = FALSE)
60 60 
     }
61 61 
     invisible(d.f.curation)
62 62 
 }
... ... 
@@ -64,16 +64,16 @@ createCurationFile <- function(file.rds, overwrite.uncurated = TRUE,
64 64 
 .getSexFromRds <- function(rds) {
65 65 
     # if run without VCF, then we don't have sex information from VCF
66 66 
     if (is.null(rds$input$sex.vcf)) return(rds$input$sex)
67 
-
67 
+
68 68 
     # conflict of coverage and snp based sex genotyper?
69 69 
     if (!is.na(rds$input$sex) && !is.na(rds$input$sex.vcf)) {
70 70 
         if (rds$input$sex == rds$input$sex.vcf) return(rds$input$sex)
71 
-        return(paste("Coverage:", rds$input$sex, "VCF:", rds$input$sex.vcf))
72 
-    }
73 
-    # believe coverage based more than VCF in case we have only limited
71 
+        return(paste("Coverage:", rds$input$sex, "VCF:", rds$input$sex.vcf))
72 
+    }
73 
+    # believe coverage based more than VCF in case we have only limited
74 74 
     # number of SNPs on chrX
75 75 
     if (!is.na(rds$input$sex)) {
76 76 
         return(rds$input$sex)
77 
-    }
77 
+    }
78 78 
     return(rds$input$sex.vcf)
79 79 
 }
Browse code

Added support for GATK4 segmentation files (#6).

Markus Riester authored on 11/08/2019 16:33:11
Showing 1 changed files
R/createCurationFile.R
History View file @ ab9bc38
1 1 
old mode 100755
2 2 
new mode 100644
Browse code

Some final code cleanup before 1.8 with lintr.

lima1 authored on 15/10/2017 00:49:40
Showing 1 changed files
R/createCurationFile.R
History View file @ e769c0f
... ... 
@@ -55,7 +55,7 @@ createCurationFile <- function(file.rds, overwrite.uncurated = TRUE,
55 55 
         } else {
56 56 
             write.csv(d.f.curation, file=filename, row.names=FALSE)
57 57 
         }
58 
-    } else {
58 
+    } else {
59 59 
         write.csv(d.f.curation, file=filename, row.names=FALSE)
60 60 
     }
61 61 
     invisible(d.f.curation)
Browse code

Fix for createCurationFile crash without VCF (https://github.com/lima1/PureCN/issues/14)

Markus Riester authored on 10/10/2017 20:58:54
Showing 1 changed files
R/createCurationFile.R
History View file @ 3841870
... ... 
@@ -62,10 +62,16 @@ createCurationFile <- function(file.rds, overwrite.uncurated = TRUE,
62 62 
 }
63 63
64 64 
 .getSexFromRds <- function(rds) {
65 
+    # if run without VCF, then we don't have sex information from VCF
66 
+    if (is.null(rds$input$sex.vcf)) return(rds$input$sex)
67 
+
68 
+    # conflict of coverage and snp based sex genotyper?
65 69 
     if (!is.na(rds$input$sex) && !is.na(rds$input$sex.vcf)) {
66 70 
         if (rds$input$sex == rds$input$sex.vcf) return(rds$input$sex)
67 71 
         return(paste("Coverage:", rds$input$sex, "VCF:", rds$input$sex.vcf))
68 72 
     }
73 
+    # believe coverage based more than VCF in case we have only limited
74 
+    # number of SNPs on chrX
69 75 
     if (!is.na(rds$input$sex)) {
70 76 
         return(rds$input$sex)
71 77 
     }
Browse code

Removed beta.model from SNV.posterior.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@126298 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 29/01/2017 01:50:31
Showing 1 changed files
R/createCurationFile.R
History View file @ fd88cb9
... ... 
@@ -27,7 +27,7 @@ createCurationFile <- function(file.rds, overwrite.uncurated = TRUE,
27 27 
     overwrite.curated=FALSE) {
28 28 
     rds <- readRDS(file.rds)
29 29 
     res <- rds$results[[1]]
30 
-    contamination <- res$SNV.posterior$beta.model$posterior.contamination
30 
+    contamination <- res$SNV.posterior$posterior.contamination
31 31 
     contamination <- if (is.null(contamination)) 0 else contamination
32 32 
     d.f.curation <- data.frame(
33 33 
         Sampleid=res$seg$ID[1],
Browse code

Skip balanced high ploidy solutions from post.optimization; other minor tweaks and documentation improvements.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@125950 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 15/01/2017 20:41:48
Showing 1 changed files
R/createCurationFile.R
History View file @ df9b8e8
... ... 
@@ -8,6 +8,8 @@
8 8 
 #' serialized with \code{saveRDS}.
9 9 
 #' @param overwrite.uncurated Overwrite existing files unless flagged as
10 10 
 #' \sQuote{Curated}.
11 
+#' @param overwrite.curated Overwrite existing files even if flagged as
12 
+#' \sQuote{Curated}.
11 13 
 #' @return A \code{data.frame} with the tumor purity and ploidy of the maximum
12 14 
 #' likelihood solution.
13 15 
 #' @author Markus Riester
... ... 
@@ -21,7 +23,8 @@
21 23 
 #'
22 24 
 #' @export createCurationFile
23 25 
 #' @importFrom utils write.csv
24 
-createCurationFile <- function(file.rds, overwrite.uncurated = TRUE) {
26 
+createCurationFile <- function(file.rds, overwrite.uncurated = TRUE,
27 
+    overwrite.curated=FALSE) {
25 28 
     rds <- readRDS(file.rds)
26 29 
     res <- rds$results[[1]]
27 30 
     contamination <- res$SNV.posterior$beta.model$posterior.contamination
... ... 
@@ -43,7 +46,7 @@ createCurationFile <- function(file.rds, overwrite.uncurated = TRUE) {
43 46
44 47 
     if (file.exists(filename)) {
45 48 
         tmp <- read.csv(filename, as.is=TRUE)
46 
-        if (tmp$Curated[1]) {
49 
+        if (tmp$Curated[1] && !overwrite.curated) {
47 50 
             warning(filename,
48 51 
                 " already exists and seems to be edited.",
49 52 
                 " Will not overwrite it.")
Browse code

Added alpha version of contamination plot.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@125771 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 09/01/2017 03:11:04
Showing 1 changed files
R/createCurationFile.R
History View file @ 5df14a2
... ... 
@@ -24,12 +24,14 @@
24 24 
 createCurationFile <- function(file.rds, overwrite.uncurated = TRUE) {
25 25 
     rds <- readRDS(file.rds)
26 26 
     res <- rds$results[[1]]
27 
-
27 
+    contamination <- res$SNV.posterior$beta.model$posterior.contamination
28 
+    contamination <- if (is.null(contamination)) 0 else contamination
28 29 
     d.f.curation <- data.frame(
29 30 
         Sampleid=res$seg$ID[1],
30 31 
         Purity=res$purity,
31 32 
         Ploidy=res$ploidy,
32 33 
         Sex=.getSexFromRds(rds),
34 
+        Contamination=contamination,
33 35 
         Flagged=res$flag,
34 36 
         Failed=FALSE,
35 37 
         Curated=FALSE,
Browse code

Switched from inlinedocs to roxygen2.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@125364 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 21/12/2016 08:33:05
Showing 1 changed files
R/createCurationFile.R
History View file @ 7d29a0b
... ... 
@@ -1,13 +1,27 @@
1 
-createCurationFile <- structure(function(# Create file to curate PureCN results
2 
-### Function to create a CSV file that can be used to mark the correct solution
3 
-### in the output of a \code{\link{runAbsoluteCN}} run.
4 
-file.rds,
5 
-### Output of the \code{\link{runAbsoluteCN}} function, serialized
6 
-### with \code{saveRDS}.
7 
-##seealso<< \code{\link{runAbsoluteCN}}
8 
-overwrite.uncurated=TRUE
9 
-### Overwrite existing files unless flagged as \sQuote{Curated}.
10 
-) {
1 
+#' Create file to curate PureCN results
2 
+#'
3 
+#' Function to create a CSV file that can be used to mark the correct solution
4 
+#' in the output of a \code{\link{runAbsoluteCN}} run.
5 
+#'
6 
+#'
7 
+#' @param file.rds Output of the \code{\link{runAbsoluteCN}} function,
8 
+#' serialized with \code{saveRDS}.
9 
+#' @param overwrite.uncurated Overwrite existing files unless flagged as
10 
+#' \sQuote{Curated}.
11 
+#' @return A \code{data.frame} with the tumor purity and ploidy of the maximum
12 
+#' likelihood solution.
13 
+#' @author Markus Riester
14 
+#' @seealso \code{\link{runAbsoluteCN}}
15 
+#' @examples
16 
+#'
17 
+#' data(purecn.example.output)
18 
+#' file.rds <- "Sample1_PureCN.rds"
19 
+#' saveRDS(purecn.example.output, file=file.rds)
20 
+#' createCurationFile(file.rds)
21 
+#'
22 
+#' @export createCurationFile
23 
+#' @importFrom utils write.csv
24 
+createCurationFile <- function(file.rds, overwrite.uncurated = TRUE) {
11 25 
     rds <- readRDS(file.rds)
12 26 
     res <- rds$results[[1]]
13 27
... ... 
@@ -40,14 +54,7 @@ overwrite.uncurated=TRUE
40 54 
         write.csv(d.f.curation, file=filename, row.names=FALSE)
41 55 
     }
42 56 
     invisible(d.f.curation)
43 
-### A \code{data.frame} with the tumor purity and ploidy of the
44 
-### maximum likelihood solution.
45 
-},ex=function() {
46 
-data(purecn.example.output)
47 
-file.rds <- "Sample1_PureCN.rds"
48 
-saveRDS(purecn.example.output, file=file.rds)
49 
-createCurationFile(file.rds)
50 
-})
57 
+}
51 58
52 59 
 .getSexFromRds <- function(rds) {
53 60 
     if (!is.na(rds$input$sex) && !is.na(rds$input$sex.vcf)) {
... ... 
@@ -59,4 +66,3 @@ createCurationFile(file.rds)
59 66 
     }
60 67 
     return(rds$input$sex.vcf)
61 68 
 }
62 
-
Browse code

Use double over single quotes.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@124685 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 01/12/2016 03:58:10
Showing 1 changed files
R/createCurationFile.R
History View file @ aaee9a7
... ... 
@@ -44,7 +44,7 @@ overwrite.uncurated=TRUE
44 44 
 ### maximum likelihood solution.
45 45 
 },ex=function() {
46 46 
 data(purecn.example.output)
47 
-file.rds <- 'Sample1_PureCN.rds'
47 
+file.rds <- "Sample1_PureCN.rds"
48 48 
 saveRDS(purecn.example.output, file=file.rds)
49 49 
 createCurationFile(file.rds)
50 50 
 })
Browse code

Interval padding.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@122964 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 23/10/2016 01:42:13
Showing 1 changed files
R/createCurationFile.R
History View file @ 644da9f
... ... 
@@ -8,12 +8,14 @@ file.rds,
8 8 
 overwrite.uncurated=TRUE
9 9 
 ### Overwrite existing files unless flagged as \sQuote{Curated}.
10 10 
 ) {
11 
-    res <- readRDS(file.rds)$results[[1]]
11 
+    rds <- readRDS(file.rds)
12 
+    res <- rds$results[[1]]
12 13
13 14 
     d.f.curation <- data.frame(
14 15 
         Sampleid=res$seg$ID[1],
15 16 
         Purity=res$purity,
16 17 
         Ploidy=res$ploidy,
18 
+        Sex=.getSexFromRds(rds),
17 19 
         Flagged=res$flag,
18 20 
         Failed=FALSE,
19 21 
         Curated=FALSE,
... ... 
@@ -46,3 +48,15 @@ file.rds <- 'Sample1_PureCN.rds'
46 48 
 saveRDS(purecn.example.output, file=file.rds)
47 49 
 createCurationFile(file.rds)
48 50 
 })
51 
+
52 
+.getSexFromRds <- function(rds) {
53 
+    if (!is.na(rds$input$sex) && !is.na(rds$input$sex.vcf)) {
54 
+        if (rds$input$sex == rds$input$sex.vcf) return(rds$input$sex)
55 
+        return(paste("Coverage:", rds$input$sex, "VCF:", rds$input$sex.vcf))
56 
+    }
57 
+    if (!is.na(rds$input$sex)) {
58 
+        return(rds$input$sex)
59 
+    }
60 
+    return(rds$input$sex.vcf)
61 
+}
62 
+
Browse code

Added support for 100% pure samples in matched normal mode; Code cleanups; Polishing of manpages.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@119603 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 24/07/2016 21:05:26
Showing 1 changed files
R/createCurationFile.R
History View file @ 74e1130
... ... 
@@ -6,7 +6,7 @@ file.rds,
6 6 
 ### with \code{saveRDS}.
7 7 
 ##seealso<< \code{\link{runAbsoluteCN}}
8 8 
 overwrite.uncurated=TRUE
9 
-### Overwrite existing files unless flagged as "Curated".
9 
+### Overwrite existing files unless flagged as \sQuote{Curated}.
10 10 
 ) {
11 11 
     res <- readRDS(file.rds)$results[[1]]
12 12
... ... 
@@ -38,8 +38,8 @@ overwrite.uncurated=TRUE
38 38 
         write.csv(d.f.curation, file=filename, row.names=FALSE)
39 39 
     }
40 40 
     invisible(d.f.curation)
41 
-###A data.frame with the tumor purity and ploidy of the maximum likelihood
42 
-###solution.
41 
+### A \code{data.frame} with the tumor purity and ploidy of the
42 
+### maximum likelihood solution.
43 43 
 },ex=function() {
44 44 
 data(purecn.example.output)
45 45 
 file.rds <- 'Sample1_PureCN.rds'
Browse code

Formatting of function names and code in manpages.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@119236 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 09/07/2016 23:14:53
Showing 1 changed files
R/createCurationFile.R
History View file @ 566e4a3
... ... 
@@ -1,8 +1,10 @@
1 1 
 createCurationFile <- structure(function(# Create file to curate PureCN results
2 2 
 ### Function to create a CSV file that can be used to mark the correct solution
3 
-### in the output of a runAbsoluteCN() run.
3 
+### in the output of a \code{\link{runAbsoluteCN}} run.
4 4 
 file.rds,
5 
-### Output of the runAbsoluteCN() function, serialized with saveRDS()
5 
+### Output of the \code{\link{runAbsoluteCN}} function, serialized
6 
+### with \code{saveRDS}.
7 
+##seealso<< \code{\link{runAbsoluteCN}}
6 8 
 overwrite.uncurated=TRUE
7 9 
 ### Overwrite existing files unless flagged as "Curated".
8 10 
 ) {
... ... 
@@ -37,7 +39,7 @@ overwrite.uncurated=TRUE
37 39 
     }
38 40 
     invisible(d.f.curation)
39 41 
 ###A data.frame with the tumor purity and ploidy of the maximum likelihood
40 
-###solution
42 
+###solution.
41 43 
 },ex=function() {
42 44 
 data(purecn.example.output)
43 45 
 file.rds <- 'Sample1_PureCN.rds'
Browse code

fixed newly introduced bug in .strip.chr.name, more code cleanups

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@116407 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 17/04/2016 05:14:08
Showing 1 changed files
R/createCurationFile.R
History View file @ 3c2bdd9
... ... 
@@ -24,10 +24,11 @@ overwrite.uncurated=TRUE
24 24 
     if (file.exists(filename)) {
25 25 
         tmp <- read.csv(filename, as.is=TRUE)
26 26 
         if (tmp$Curated[1]) {
27 
-            warning(paste(filename,
28 
-                "already exists and seems to be edited. Will not overwrite it."))
27 
+            warning(filename,
28 
+                " already exists and seems to be edited.",
29 
+                " Will not overwrite it.")
29 30 
         } else if (!overwrite.uncurated) {
30 
-            warning(paste(filename, "already exists. Will not overwrite it."))
31 
+            warning(filename, " already exists. Will not overwrite it.")
31 32 
         } else {
32 33 
             write.csv(d.f.curation, file=filename, row.names=FALSE)
33 34 
         }
Browse code

shorten lines to 80 characters

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@116399 bc3139a8-67e5-0310-9ffc-ced21a209358

Markus Riester authored on 16/04/2016 23:19:25
Showing 1 changed files
R/createCurationFile.R
History View file @ dce9fe0
... ... 
@@ -24,7 +24,8 @@ overwrite.uncurated=TRUE
24 24 
     if (file.exists(filename)) {
25 25 
         tmp <- read.csv(filename, as.is=TRUE)
26 26 
         if (tmp$Curated[1]) {
27 
-            warning(paste(filename, "already exists and seems to be edited. Will not overwrite it."))
27 
+            warning(paste(filename,
28 
+                "already exists and seems to be edited. Will not overwrite it."))
28 29 
         } else if (!overwrite.uncurated) {
29 30 
             warning(paste(filename, "already exists. Will not overwrite it."))
30 31 
         } else {
... ... 
@@ -33,7 +34,7 @@ overwrite.uncurated=TRUE
33 34 
     } else {
34 35 
         write.csv(d.f.curation, file=filename, row.names=FALSE)
35 36 
     }
36 
-    d.f.curation
37 
+    invisible(d.f.curation)
37 38 
 ###A data.frame with the tumor purity and ploidy of the maximum likelihood
38 39 
 ###solution
39 40 
 },ex=function() {
... ... 
@@ -41,4 +42,4 @@ data(purecn.example.output)
41 42 
 file.rds <- 'Sample1_PureCN.rds'
42 43 
 saveRDS(purecn.example.output, file=file.rds)
43 44 
 createCurationFile(file.rds)
44 
-})
45 
+})
Browse code

Adding PureCN, MultiDataSet, Harman

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PureCN@116291 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 14/04/2016 20:21:39
Showing 1 changed files
R/createCurationFile.R
History View file @ ea58a45
1 1 
new file mode 100755
... ... 
@@ -0,0 +1,44 @@
1 
+createCurationFile <- structure(function(# Create file to curate PureCN results
2 
+### Function to create a CSV file that can be used to mark the correct solution
3 
+### in the output of a runAbsoluteCN() run.
4 
+file.rds,
5 
+### Output of the runAbsoluteCN() function, serialized with saveRDS()
6 
+overwrite.uncurated=TRUE
7 
+### Overwrite existing files unless flagged as "Curated".
8 
+) {
9 
+    res <- readRDS(file.rds)$results[[1]]
10 
+
11 
+    d.f.curation <- data.frame(
12 
+        Sampleid=res$seg$ID[1],
13 
+        Purity=res$purity,
14 
+        Ploidy=res$ploidy,
15 
+        Flagged=res$flag,
16 
+        Failed=FALSE,
17 
+        Curated=FALSE,
18 
+        Comment=res$flag_comment
19 
+    )
20 
+
21 
+    filename <- file.path(dirname(file.rds),
22 
+        paste(gsub(".rds$", "", basename(file.rds)), "csv", sep="."))
23 
+
24 
+    if (file.exists(filename)) {
25 
+        tmp <- read.csv(filename, as.is=TRUE)
26 
+        if (tmp$Curated[1]) {
27 
+            warning(paste(filename, "already exists and seems to be edited. Will not overwrite it."))
28 
+        } else if (!overwrite.uncurated) {
29 
+            warning(paste(filename, "already exists. Will not overwrite it."))
30 
+        } else {
31 
+            write.csv(d.f.curation, file=filename, row.names=FALSE)
32 
+        }
33 
+    } else {
34 
+        write.csv(d.f.curation, file=filename, row.names=FALSE)
35 
+    }
36 
+    d.f.curation
37 
+###A data.frame with the tumor purity and ploidy of the maximum likelihood
38 
+###solution
39 
+},ex=function() {
40 
+data(purecn.example.output)
41 
+file.rds <- 'Sample1_PureCN.rds'
42 
+saveRDS(purecn.example.output, file=file.rds)
43 
+createCurationFile(file.rds)
44 
+})