1. basecallQC
  2. R
  3. tables.R
Browse code

Fixes and updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/basecallQC@130196 bc3139a8-67e5-0310-9ffc-ced21a209358

Tom Carroll authored on 08/06/2017 16:16:28
Showing 1 changed files
R/tables.R
History View file @ 5e9aab2
... ... 
@@ -1,165 +1,165 @@
1 
-#' Generate an HTML table of per sample summary demultiplexing statistics
2 
-#'
3 
-#' @usage
4 
-#' \S4method{summaryDemuxTable}{baseCallQC}(object)
5 
-#'
6 
-#' @docType methods
7 
-#' @name summaryDemuxTable
8 
-#' @rdname summaryDemuxTable
9 
-#' @aliases summaryDemuxTable summaryDemuxTable,baseCallQC-method
10 
-#' @author Thomas Carroll
11 
-#'
12 
-#' @param object A  basecallQC object or list from call to demultiplexMetrics()
13 
-#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
14 
-#' @return  An HTML table for reporting demultiplexing results.
15 
-#' @import stringr XML RColorBrewer methods raster
16 
-#' @examples
17 
-#'
18 
-#' fileLocations <- system.file("extdata",package="basecallQC")
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-#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
20 
-#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
21 
-#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
22 
-#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
23 
-#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
24 
-#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
25 
-#' summaryDemuxTable(bclQC,output="static")
26 
-#' @export
27 
-summaryDemuxTable.basecallQC <- function(object,output="static"){
28 
-
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-  toTable <- object@demultiplexMetrics$summarisedDemuxStats$Summary
30 
-  if(output=="static"){
31 
-    return(kable(toTable))
32 
-  }
33 
-  if(output=="html"){
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-    return(DT::datatable(toTable))
35 
-  }
36 
-}
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-
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-
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-setGeneric("summaryDemuxTable", function(object="basecallQC",output="character") standardGeneric("summaryDemuxTable"))
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-
41 
-#' @rdname summaryDemuxTable
42 
-#' @export
43 
-setMethod("summaryDemuxTable", signature(object="basecallQC"), summaryDemuxTable.basecallQC)
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-
45 
-
46 
-summaryDemuxTable.list <- function(object,output="static"){
47 
-  toTable <- object$summarisedDemuxStats$Summary
48 
-  if(output=="static"){
49 
-    return(kable(toTable))
50 
-  }
51 
-  if(output=="html"){
52 
-    return(DT::datatable(toTable))
53 
-  }
54 
-}
55 
-
56 
-#' @rdname summaryDemuxTable
57 
-#' @export
58 
-setMethod("summaryDemuxTable", signature(object="list"),summaryDemuxTable.list)
59 
-
60 
-
61 
-
62 
-
63 
-
64 
-#' Creates an HTML table of per sample summary statistics from basecalling results
65 
-#'
66 
-#' @usage
67 
-#' \S4method{summaryConvStatsTable}{baseCallQC}(object)
68 
-#'
69 
-#' @docType methods
70 
-#' @name summaryConvStatsTable
71 
-#' @rdname summaryConvStatsTable
72 
-#' @aliases summaryConvStatsTable summaryConvStatsTable,baseCallQC-method
73 
-#' @author Thomas Carroll
74 
-#'
75 
-#' @param object A  basecallQC object or list from call to baseCallMetrics()
76 
-#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
77 
-#' @return An HTML table for reporting basecalling results.
78 
-#' @import stringr XML RColorBrewer methods raster
79 
-#' @examples
80 
-#'
81 
-#' fileLocations <- system.file("extdata",package="basecallQC")
82 
-#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
83 
-#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
84 
-#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
85 
-#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
86 
-#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
87 
-#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
88 
-#' summaryDemuxTable(bclQC,output="static")
89 
-#' @export
90 
-summaryConvStatsTable.basecallQC <- function(object,output="static"){
91 
-
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-  toTable <- object@baseCallMetrics$summarisedConvStats$Sample_Stats
93 
-  if(output=="static"){
94 
-    return(kable(toTable))
95 
-  }
96 
-  if(output=="html"){
97 
-    return(DT::datatable(toTable))
98 
-  }
99 
-}
100 
-
101 
-setGeneric("summaryConvStatsTable", function(object="basecallQC",output="character") standardGeneric("summaryConvStatsTable"))
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-
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-#' @rdname summaryConvStatsTable
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-#' @export
105 
-setMethod("summaryConvStatsTable", signature(object="basecallQC"), summaryConvStatsTable.basecallQC)
106 
-
107 
-
108 
-summaryConvStatsTable.list <- function(object,output="static"){
109 
-
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-  toTable <- object$summarisedConvStats$Sample_Stats
111 
-  if(output=="static"){
112 
-    return(kable(toTable))
113 
-  }
114 
-  if(output=="html"){
115 
-    return(DT::datatable(toTable))
116 
-  }
117 
-}
118 
-
119 
-#' @rdname summaryConvStatsTable
120 
-#' @export
121 
-setMethod("summaryConvStatsTable", signature(object="list"),summaryConvStatsTable.list)
122 
-
123 
-
124 
-#' Generate an HTML table linking to per sample summary fastq QC statistics from ShortRead
125 
-#'
126 
-#' Creates an HTML table linking to per sample summary fastq QC statistics from ShortRead
127 
-#'
128 
-#'
129 
-#' @docType methods
130 
-#' @name makeFQTable
131 
-#' @rdname makeFQTable
132 
-#'
133 
-#' @author Thomas Carroll
134 
-#'
135 
-#' @param object A basecall QC object as returned from basecallQC function
136 
-#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
137 
-#' @return A HTML table for reporting fastq QC results from ShortRead.
138 
-#' Table contains read counts and links to ShortRead QA reports per sample.
139 
-#' @import stringr XML RColorBrewer methods raster
140 
-#' @examples
141 
-#'
142 
-#' fileLocations <- system.file("extdata",package="basecallQC")
143 
-#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
144 
-#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
145 
-#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
146 
-#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
147 
-#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
148 
-#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
149 
-#' #makeFQTable(bclQC,output="static")
150 
-#' @export
151 
-
152 
-makeFQTable <- function(object,output="static"){
153 
-  fqQCTable <- object@fqQCmetrics$FQQC_Table
154 
-    if(!is.null(fqQCTable)){
155 
-      if(output=="static"){
156 
-        table <- kable(fqQCTable,escape = FALSE)
157 
-      }
158 
-      if(output=="html"){
159 
-        table <- DT::datatable(fqQCTable,escape=FALSE)
160 
-      }
161 
-      return(table)
162 
-    }else{
163 
-      return(NULL)
164 
-  }
165 
-}
1 
+#' Generate an HTML table of per sample summary demultiplexing statistics
2 
+#'
3 
+#' @usage
4 
+#' \S4method{summaryDemuxTable}{baseCallQC}(object)
5 
+#'
6 
+#' @docType methods
7 
+#' @name summaryDemuxTable
8 
+#' @rdname summaryDemuxTable
9 
+#' @aliases summaryDemuxTable summaryDemuxTable,baseCallQC-method
10 
+#' @author Thomas Carroll
11 
+#'
12 
+#' @param object A  basecallQC object or list from call to demultiplexMetrics()
13 
+#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
14 
+#' @return  An HTML table for reporting demultiplexing results.
15 
+#' @import stringr XML RColorBrewer methods raster
16 
+#' @examples
17 
+#'
18 
+#' fileLocations <- system.file("extdata",package="basecallQC")
19 
+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
20 
+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
21 
+#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
22 
+#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
23 
+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
24 
+#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
25 
+#' summaryDemuxTable(bclQC,output="static")
26 
+#' @export
27 
+summaryDemuxTable.basecallQC <- function(object,output="static"){
28 
+
29 
+  toTable <- object@demultiplexMetrics$summarisedDemuxStats$Summary
30 
+  if(output=="static"){
31 
+    return(kable(toTable))
32 
+  }
33 
+  if(output=="html"){
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+    return(DT::datatable(toTable))
35 
+  }
36 
+}
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+
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+
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+setGeneric("summaryDemuxTable", function(object="basecallQC",output="character") standardGeneric("summaryDemuxTable"))
40 
+
41 
+#' @rdname summaryDemuxTable
42 
+#' @export
43 
+setMethod("summaryDemuxTable", signature(object="basecallQC"), summaryDemuxTable.basecallQC)
44 
+
45 
+
46 
+summaryDemuxTable.list <- function(object,output="static"){
47 
+  toTable <- object$summarisedDemuxStats$Summary
48 
+  if(output=="static"){
49 
+    return(kable(toTable))
50 
+  }
51 
+  if(output=="html"){
52 
+    return(DT::datatable(toTable))
53 
+  }
54 
+}
55 
+
56 
+#' @rdname summaryDemuxTable
57 
+#' @export
58 
+setMethod("summaryDemuxTable", signature(object="list"),summaryDemuxTable.list)
59 
+
60 
+
61 
+
62 
+
63 
+
64 
+#' Creates an HTML table of per sample summary statistics from basecalling results
65 
+#'
66 
+#' @usage
67 
+#' \S4method{summaryConvStatsTable}{baseCallQC}(object)
68 
+#'
69 
+#' @docType methods
70 
+#' @name summaryConvStatsTable
71 
+#' @rdname summaryConvStatsTable
72 
+#' @aliases summaryConvStatsTable summaryConvStatsTable,baseCallQC-method
73 
+#' @author Thomas Carroll
74 
+#'
75 
+#' @param object A  basecallQC object or list from call to baseCallMetrics()
76 
+#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
77 
+#' @return An HTML table for reporting basecalling results.
78 
+#' @import stringr XML RColorBrewer methods raster
79 
+#' @examples
80 
+#'
81 
+#' fileLocations <- system.file("extdata",package="basecallQC")
82 
+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
83 
+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
84 
+#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
85 
+#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
86 
+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
87 
+#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
88 
+#' summaryDemuxTable(bclQC,output="static")
89 
+#' @export
90 
+summaryConvStatsTable.basecallQC <- function(object,output="static"){
91 
+
92 
+  toTable <- object@baseCallMetrics$summarisedConvStats$Sample_Stats
93 
+  if(output=="static"){
94 
+    return(kable(toTable))
95 
+  }
96 
+  if(output=="html"){
97 
+    return(DT::datatable(toTable))
98 
+  }
99 
+}
100 
+
101 
+setGeneric("summaryConvStatsTable", function(object="basecallQC",output="character") standardGeneric("summaryConvStatsTable"))
102 
+
103 
+#' @rdname summaryConvStatsTable
104 
+#' @export
105 
+setMethod("summaryConvStatsTable", signature(object="basecallQC"), summaryConvStatsTable.basecallQC)
106 
+
107 
+
108 
+summaryConvStatsTable.list <- function(object,output="static"){
109 
+
110 
+  toTable <- object$summarisedConvStats$Sample_Stats
111 
+  if(output=="static"){
112 
+    return(kable(toTable))
113 
+  }
114 
+  if(output=="html"){
115 
+    return(DT::datatable(toTable))
116 
+  }
117 
+}
118 
+
119 
+#' @rdname summaryConvStatsTable
120 
+#' @export
121 
+setMethod("summaryConvStatsTable", signature(object="list"),summaryConvStatsTable.list)
122 
+
123 
+
124 
+#' Generate an HTML table linking to per sample summary fastq QC statistics from ShortRead
125 
+#'
126 
+#' Creates an HTML table linking to per sample summary fastq QC statistics from ShortRead
127 
+#'
128 
+#'
129 
+#' @docType methods
130 
+#' @name makeFQTable
131 
+#' @rdname makeFQTable
132 
+#'
133 
+#' @author Thomas Carroll
134 
+#'
135 
+#' @param object A basecall QC object as returned from basecallQC function
136 
+#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
137 
+#' @return A HTML table for reporting fastq QC results from ShortRead.
138 
+#' Table contains read counts and links to ShortRead QA reports per sample.
139 
+#' @import stringr XML RColorBrewer methods raster
140 
+#' @examples
141 
+#'
142 
+#' fileLocations <- system.file("extdata",package="basecallQC")
143 
+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
144 
+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
145 
+#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
146 
+#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
147 
+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
148 
+#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
149 
+#' #makeFQTable(bclQC,output="static")
150 
+#' @export
151 
+
152 
+makeFQTable <- function(object,output="static"){
153 
+  fqQCTable <- object@fqQCmetrics$FQQC_Table
154 
+    if(!is.null(fqQCTable)){
155 
+      if(output=="static"){
156 
+        table <- kable(fqQCTable,escape = FALSE)
157 
+      }
158 
+      if(output=="html"){
159 
+        table <- DT::datatable(fqQCTable,escape=FALSE)
160 
+      }
161 
+      return(table)
162 
+    }else{
163 
+      return(NULL)
164 
+  }
165 
+}
Browse code

Adding RaggedExperiment, basecallQC, CATALYST, GenomicScores, IMAS, semisup, ImpulseDE2, methylInheritance, biotmle, biotmleData, BLMA, TCGAWorkflow, metavizr

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/basecallQC@128350 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 07/04/2017 20:14:00
Showing 1 changed files
R/tables.R
History View file @ 82d9bc8
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,165 @@
1 
+#' Generate an HTML table of per sample summary demultiplexing statistics
2 
+#'
3 
+#' @usage
4 
+#' \S4method{summaryDemuxTable}{baseCallQC}(object)
5 
+#'
6 
+#' @docType methods
7 
+#' @name summaryDemuxTable
8 
+#' @rdname summaryDemuxTable
9 
+#' @aliases summaryDemuxTable summaryDemuxTable,baseCallQC-method
10 
+#' @author Thomas Carroll
11 
+#'
12 
+#' @param object A  basecallQC object or list from call to demultiplexMetrics()
13 
+#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
14 
+#' @return  An HTML table for reporting demultiplexing results.
15 
+#' @import stringr XML RColorBrewer methods raster
16 
+#' @examples
17 
+#'
18 
+#' fileLocations <- system.file("extdata",package="basecallQC")
19 
+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
20 
+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
21 
+#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
22 
+#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
23 
+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
24 
+#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
25 
+#' summaryDemuxTable(bclQC,output="static")
26 
+#' @export
27 
+summaryDemuxTable.basecallQC <- function(object,output="static"){
28 
+
29 
+  toTable <- object@demultiplexMetrics$summarisedDemuxStats$Summary
30 
+  if(output=="static"){
31 
+    return(kable(toTable))
32 
+  }
33 
+  if(output=="html"){
34 
+    return(DT::datatable(toTable))
35 
+  }
36 
+}
37 
+
38 
+
39 
+setGeneric("summaryDemuxTable", function(object="basecallQC",output="character") standardGeneric("summaryDemuxTable"))
40 
+
41 
+#' @rdname summaryDemuxTable
42 
+#' @export
43 
+setMethod("summaryDemuxTable", signature(object="basecallQC"), summaryDemuxTable.basecallQC)
44 
+
45 
+
46 
+summaryDemuxTable.list <- function(object,output="static"){
47 
+  toTable <- object$summarisedDemuxStats$Summary
48 
+  if(output=="static"){
49 
+    return(kable(toTable))
50 
+  }
51 
+  if(output=="html"){
52 
+    return(DT::datatable(toTable))
53 
+  }
54 
+}
55 
+
56 
+#' @rdname summaryDemuxTable
57 
+#' @export
58 
+setMethod("summaryDemuxTable", signature(object="list"),summaryDemuxTable.list)
59 
+
60 
+
61 
+
62 
+
63 
+
64 
+#' Creates an HTML table of per sample summary statistics from basecalling results
65 
+#'
66 
+#' @usage
67 
+#' \S4method{summaryConvStatsTable}{baseCallQC}(object)
68 
+#'
69 
+#' @docType methods
70 
+#' @name summaryConvStatsTable
71 
+#' @rdname summaryConvStatsTable
72 
+#' @aliases summaryConvStatsTable summaryConvStatsTable,baseCallQC-method
73 
+#' @author Thomas Carroll
74 
+#'
75 
+#' @param object A  basecallQC object or list from call to baseCallMetrics()
76 
+#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
77 
+#' @return An HTML table for reporting basecalling results.
78 
+#' @import stringr XML RColorBrewer methods raster
79 
+#' @examples
80 
+#'
81 
+#' fileLocations <- system.file("extdata",package="basecallQC")
82 
+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
83 
+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
84 
+#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
85 
+#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
86 
+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
87 
+#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
88 
+#' summaryDemuxTable(bclQC,output="static")
89 
+#' @export
90 
+summaryConvStatsTable.basecallQC <- function(object,output="static"){
91 
+
92 
+  toTable <- object@baseCallMetrics$summarisedConvStats$Sample_Stats
93 
+  if(output=="static"){
94 
+    return(kable(toTable))
95 
+  }
96 
+  if(output=="html"){
97 
+    return(DT::datatable(toTable))
98 
+  }
99 
+}
100 
+
101 
+setGeneric("summaryConvStatsTable", function(object="basecallQC",output="character") standardGeneric("summaryConvStatsTable"))
102 
+
103 
+#' @rdname summaryConvStatsTable
104 
+#' @export
105 
+setMethod("summaryConvStatsTable", signature(object="basecallQC"), summaryConvStatsTable.basecallQC)
106 
+
107 
+
108 
+summaryConvStatsTable.list <- function(object,output="static"){
109 
+
110 
+  toTable <- object$summarisedConvStats$Sample_Stats
111 
+  if(output=="static"){
112 
+    return(kable(toTable))
113 
+  }
114 
+  if(output=="html"){
115 
+    return(DT::datatable(toTable))
116 
+  }
117 
+}
118 
+
119 
+#' @rdname summaryConvStatsTable
120 
+#' @export
121 
+setMethod("summaryConvStatsTable", signature(object="list"),summaryConvStatsTable.list)
122 
+
123 
+
124 
+#' Generate an HTML table linking to per sample summary fastq QC statistics from ShortRead
125 
+#'
126 
+#' Creates an HTML table linking to per sample summary fastq QC statistics from ShortRead
127 
+#'
128 
+#'
129 
+#' @docType methods
130 
+#' @name makeFQTable
131 
+#' @rdname makeFQTable
132 
+#'
133 
+#' @author Thomas Carroll
134 
+#'
135 
+#' @param object A basecall QC object as returned from basecallQC function
136 
+#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
137 
+#' @return A HTML table for reporting fastq QC results from ShortRead.
138 
+#' Table contains read counts and links to ShortRead QA reports per sample.
139 
+#' @import stringr XML RColorBrewer methods raster
140 
+#' @examples
141 
+#'
142 
+#' fileLocations <- system.file("extdata",package="basecallQC")
143 
+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
144 
+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
145 
+#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
146 
+#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
147 
+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
148 
+#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
149 
+#' #makeFQTable(bclQC,output="static")
150 
+#' @export
151 
+
152 
+makeFQTable <- function(object,output="static"){
153 
+  fqQCTable <- object@fqQCmetrics$FQQC_Table
154 
+    if(!is.null(fqQCTable)){
155 
+      if(output=="static"){
156 
+        table <- kable(fqQCTable,escape = FALSE)
157 
+      }
158 
+      if(output=="html"){
159 
+        table <- DT::datatable(fqQCTable,escape=FALSE)
160 
+      }
161 
+      return(table)
162 
+    }else{
163 
+      return(NULL)
164 
+  }
165 
+}