AdultGbmTcga<-cBioDataPack('gbm_tcga', ask=FALSE)
Study file in cache: gbm_tcga
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_cna_hg19.seg
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_cna.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_linear_cna.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_methylation_hm27.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_methylation_hm450.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_affymetrix_microarray_zscores_ref_all_samples.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_affymetrix_microarray_zscores_ref_diploid_samples.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_affymetrix_microarray.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_agilent_microarray_zscores_ref_all_samples.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_agilent_microarray_zscores_ref_diploid_samples.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_agilent_microarray.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_seq_v2_rsem.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mutations.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mutsig.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_rppa_zscores.txt
Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_rppa.txt
harmonizing input:
removing 7 colData rownames not in sampleMap 'primary'
Warning messages:
1: In .find_with_xfix(df_colnames, get(paste0(fix, 1)), get(paste0(fix, :
Multiple prefixes found, using keyword 'region' or taking first one
2: In .find_with_xfix(df_colnames, get(paste0(fix, 1)), get(paste0(fix, :
Multiple prefixes found, using keyword 'region' or taking first one
AdultGbmTcga
A MultiAssayExperiment object of 17 listed
experiments with user-defined names and respective classes.
Containing an Error in vapply(x, [, integer(1L), pos) : values must be length 1,
but FUN(X[[1]]) result is length 0
The output errors mid-statement. Any idea what could be causing this?
AdultGbmTcga<-cBioDataPack('gbm_tcga', ask=FALSE) Study file in cache: gbm_tcga Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_cna_hg19.seg Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_cna.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_linear_cna.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_methylation_hm27.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_methylation_hm450.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_affymetrix_microarray_zscores_ref_all_samples.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_affymetrix_microarray_zscores_ref_diploid_samples.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_affymetrix_microarray.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_agilent_microarray_zscores_ref_all_samples.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_agilent_microarray_zscores_ref_diploid_samples.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_agilent_microarray.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_seq_v2_rsem_zscores_ref_all_samples.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_seq_v2_rsem_zscores_ref_diploid_samples.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mrna_seq_v2_rsem.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mutations.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_mutsig.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_rppa_zscores.txt Working on: /var/folders/hj/1wvjfb692c3gswybcg8xdcwm0000gn/T//RtmpwlOxuy/ad553abda11_gbm_tcga/gbm_tcga/data_rppa.txt harmonizing input: removing 7 colData rownames not in sampleMap 'primary' Warning messages: 1: In .find_with_xfix(df_colnames, get(paste0(fix, 1)), get(paste0(fix, : Multiple prefixes found, using keyword 'region' or taking first one 2: In .find_with_xfix(df_colnames, get(paste0(fix, 1)), get(paste0(fix, : Multiple prefixes found, using keyword 'region' or taking first one
The output errors mid-statement. Any idea what could be causing this?