Question: Problem in using TCGAvisualize_meanMethylation() function?
0
gravatar for mahmood.amiri225
21 months ago by
mahmood.amiri2250 wrote:

Hi, I used ‘TCGAbiolinks’ version 2.6.12. I have just tried to plot using TCGAvisualize_meanMethylation function, using flowing codes, but the R script didn't work well and flowing error came out. how can I solve this problem?

Thanks in advance!

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"

Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

> library(TCGAbiolinks)
> library(stringr)
> library("SummarizedExperiment")

> # Samples
> matched_met_exp <- function(project, n = NULL){
+ # get primary solid tumor samples: DNA methylation
+ message("Download DNA methylation information")
+ met450k <- GDCquery(project = project,
+                     data.category = "DNA methylation",
+                     platform = "Illumina Human Methylation 450",
+                     legacy = TRUE,
+                     sample.type = c("Primary solid Tumor"))
+ met450k.tp <- met450k$results[[1]]$cases
+ # get primary solid tumor samples: RNAseq
+ message("Download gene expression information")
+ exp <- GDCquery(project = project,
+                 data.category = "Gene expression",
+                 data.type = "Gene expression quantification",
+                 platform = "Illumina HiSeq",
+                 file.type = "results",
+                 sample.type = c("Primary solid Tumor"),
+ legacy = TRUE)
+ exp.tp <- exp$results[[1]]$cases
+ print(exp.tp[1:10])
+ # Get patients with samples in both platforms
+ patients <- unique(substr(exp.tp,1,15)[substr(exp.tp,1,12) %in% substr(met450k.tp,1,12)])
+ if(!is.null(n)) patients <- patients[1:n] # get only n samples
+ return(patients)
+ }
> lgg.samples <- matched_met_exp("TCGA-LGG", n = 10)
Download DNA methylation information
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-LGG
--------------------
oo Filtering results
--------------------
ooo By platform
ooo By sample.type
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
Download gene expression information
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-LGG
--------------------
oo Filtering results
--------------------
ooo By platform
ooo By data.type
ooo By file.type
ooo By sample.type
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
 [1] "TCGA-HT-7480-01A-11R-2090-07" "TCGA-QH-A6XC-01A-12R-A32Q-07"
 [3] "TCGA-HT-A614-01A-11R-A29R-07" "TCGA-HT-8104-01A-11R-2404-07"
 [5] "TCGA-TQ-A7RG-01A-11R-A33Z-07" "TCGA-HW-7487-01A-11R-2027-07"
 [7] "TCGA-FG-8186-01A-11R-2256-07" "TCGA-P5-A5EX-01A-12R-A28M-07"
 [9] "TCGA-CS-6667-01A-12R-2027-07" "TCGA-DU-7304-01A-12R-2090-07"
> gbm.samples <- matched_met_exp("TCGA-GBM", n = 10)
Download DNA methylation information
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-GBM
--------------------
oo Filtering results
--------------------
ooo By platform
ooo By sample.type
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
Download gene expression information
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-GBM
--------------------
oo Filtering results
--------------------
ooo By platform
ooo By data.type
ooo By file.type
ooo By sample.type
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
 [1] "TCGA-06-0184-01A-01R-1849-01" "TCGA-06-0649-01B-01R-1849-01"
 [3] "TCGA-02-2485-01A-01R-1849-01" "TCGA-26-5136-01B-01R-1850-01"
 [5] "TCGA-76-4925-01A-01R-1850-01" "TCGA-32-2632-01A-01R-1850-01"
 [7] "TCGA-06-5858-01A-01R-1849-01" "TCGA-28-5213-01A-01R-1850-01"
 [9] "TCGA-06-0157-01A-01R-1849-01" "TCGA-16-0846-01A-01R-1850-01"
> samples <- c(lgg.samples,gbm.samples)
> query.lgg <- GDCquery(project = "TCGA-LGG",
+                       data.category = "DNA methylation",
+                       platform = "Illumina Human Methylation 450",
+                       legacy = TRUE, barcode = lgg.samples)
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-LGG
--------------------
oo Filtering results
--------------------
ooo By platform
ooo By barcode
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
> met.lgg <-GDCprepare(query.lgg, save = FALSE)
  |====================================================================================| 100%Downloading genome information (try:0) Using: Homo sapiens genes (GRCh37.p13)
Loading from disk
Starting to add information to samples
 => Add clinical information to samples
Add FFPE information. More information at: 
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria 
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
 => Adding subtype information to samples
lgg subtype information from:doi:10.1016/j.cell.2015.12.028
> query.gbm <- GDCquery(project = "TCGA-GBM",
+                       data.category = "DNA methylation",
+                       platform = "Illumina Human Methylation 450",
+                       legacy = TRUE, barcode = gbm.samples)
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-GBM
--------------------
oo Filtering results
--------------------
ooo By platform
ooo By barcode
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
> met.gbm <- GDCprepare(query.gbm, save = FALSE)
  |====================================================================================| 100%Downloading genome information (try:0) Using: Homo sapiens genes (GRCh37.p13)
Loading from disk
Starting to add information to samples
 => Add clinical information to samples
Add FFPE information. More information at: 
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria 
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
 => Adding subtype information to samples
gbm subtype information from:doi:10.1016/j.cell.2015.12.028
> met <- SummarizedExperiment::cbind(met.lgg, met.gbm)
> met <- subset(met,subset = (rowSums(is.na(assay(met))) == 0))
> met <- subset(met,subset = !as.character(seqnames(met)) %in% c("chrNA","chrX","chrY"))
> TCGAvisualize_meanMethylation(met,
+                                  groupCol = "disease_type",
+                                  group.legend = "Groups",
+                                  filename = "mean_lgg_gbm.png",
+                                  print.pvalue = TRUE)
==================== DATA Summary ====================
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 
  'x' must be atomic

 

tcgabiolinks • 275 views
ADD COMMENTlink written 21 months ago by mahmood.amiri2250
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