Entering edit mode
Using TCGAbiolinks 2.5.9.
It seems that the GDC API might have changed something because
GDCquery("TCGA-BRCA")
Returns:
o GDCquery: Searching in GDC database
Genome of reference: hg38 Warning: 40 parsing failures. row # A tibble: 5 x 5 col row col expected actual file expected actual 1 1 8 columns 71 columns '[https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv](https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv)' file 2 2 8 columns 71 columns '[https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv](https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv)' row 3 3 8 columns 71 columns '[https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv](https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv)' col 4 4 8 columns 71 columns '[https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv](https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv)' expected 5 5 8 columns 71 columns '[https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv](https://gdc-api.nci.nih.gov/projects?size=1000&format=tsv)' ... ................. ... .............................................................................................. ........ .............................................................................................. ...... .................. [... truncated]
|disease_type.2 |disease_type.5 |disease_type.4 |disease_type.6 |
|:---------------------------|:-----------------------------------|:--------------------|:----------------------------|
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|Thymic Epithelial Neoplasms |Complex Mixed and Stromal Neoplasms |Basal Cell Neoplasms |Ductal and Lobular Neoplasms |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
|NA |NA |NA |NA |
Error in checkProjectInput(project) : Please set a valid project argument from the column id above. Project TCGA-BRCA was not found.
In addition: Warning messages:
1: Unnamed col_types should have the same length as `col_names`. Using smaller of the two.
2: In rbind(names(probs), probs_f) : number of columns of result is not a multiple of vector length (arg 1)
3: Unknown or uninitialised column: 'project_id'.
4: Unknown or uninitialised column: 'project_id'.
It seems the problem is in the function
getGDCprojectsin file R/internal.R.Simplifying the code in
getGDCprojectsto download json only seems to solve the issue:#' @title Retrieve all GDC projects #' @description #' getGDCprojects uses the following api to get projects #' https://gdc-api.nci.nih.gov/projects #' @export #' @import readr stringr #' @examples #' projects <- getGDCprojects() #' @return A data frame with last GDC projects getGDCprojects <- function(){ url <- "https://gdc-api.nci.nih.gov/projects?size=1000&format=json" json <- fromJSON(content(GET(url), as = "text", encoding = "UTF-8"), simplifyDataFrame = TRUE) projects <- json$data$hits projects$tumor <- unlist(lapply(projects$project_id, function(x){unlist(str_split(x,"-"))[2]})) return(projects) }