Hi, for downloading TCGA-SARC transcriptome data from GDC. I used TCGAbiolinks package trough below code:

library(TCGAbiolinks);
library(SummarizedExperiment);
query <- GDCquery(project = "TCGA-SARC",sample.type = "Primary solid Tumor",
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",
                  workflow.type = "HTSeq - FPKM")
GDCdownload(query) 
data <- GDCprepare(query)
data1 <- assay(data)

Now my SARC gene expression data has just 56512 gene type by clear ensemble id. So, I checked gencode.v22 and in that I found 60483 gene type. Now, I extract protein coding genes from gencode.v22 annotation file and the number is 19814. when I get intersection between 56512 ensemble id from my SARC gene expression data and 19814 proteing code genes I get just 19509 protein coding genes in my expression data. I am really concern about 305 lost protein genes in my study. I appreciate it if anybody shares his/her comment with me about my code validation and 305 lost protein code gens. Best

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale: [1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252
[3] LCMONETARY=EnglishUnited States.1252 LCNUMERIC=C
[5] LCTIME=English_United States.1252

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] TCGAbiolinks2.14.0 sva3.34.0 genefilter1.68.0
[4] mgcv1.8-30 nlme3.1-141 SummarizedExperiment1.16.0 [7] DelayedArray0.12.0 BiocParallel1.20.0 matrixStats0.55.0
[10] Biobase2.46.0 GenomicRanges1.38.0 GenomeInfoDb1.22.0
[13] IRanges2.20.0 S4Vectors0.24.0 BiocGenerics0.32.0
[16] stringr1.4.0 dplyr0.8.3 Hmisc4.2-0
[19] ggplot23.2.1 Formula1.2-3 survival2.44-1.1
[22] lattice0.20-38 impute1.60.0 cluster2.1.0
[25] class7.3-15 MASS7.3-51.4 sqldf0.4-11
[28] RSQLite2.1.2 gsubfn0.7 proto1.0.0
[31] WGCNA1.68 fastcluster1.1.25 dynamicTreeCut_1.63-1

loaded via a namespace (and not attached): [1] backports1.1.5 circlize0.4.8 aroma.light3.16.0
[4] BiocFileCache1.10.0 plyr1.8.4 selectr0.4-1
[7] ConsensusClusterPlus1.50.0 lazyeval0.2.2 splines3.6.1
[10] robust0.4-18.1 digest0.6.23 foreach1.4.7
[13] htmltools0.4.0 GO.db3.10.0 magrittr1.5
[16] checkmate1.9.4 memoise1.1.0 fit.models0.5-14
[19] doParallel1.0.15 limma3.42.0 ComplexHeatmap2.2.0
[22] Biostrings2.54.0 readr1.3.1 annotate1.64.0
[25] R.utils2.9.0 askpass1.1 prettyunits1.0.2
[28] colorspace1.4-1 rvest0.3.4 ggrepel0.8.1
[31] blob1.2.0 rappdirs0.3.1 rrcov1.4-7
[34] xfun0.10 jsonlite1.6 tcltk3.6.1
[37] crayon1.3.4 RCurl1.95-4.12 zeallot0.1.0
[40] zoo1.8-6 iterators1.0.12 glue1.3.1
[43] survminer0.4.6 gtable0.3.0 zlibbioc1.32.0
[46] XVector0.26.0 GetoptLong0.1.7 shape1.4.4
[49] DEoptimR1.0-8 scales1.0.0 DESeq1.38.0
[52] mvtnorm1.0-11 edgeR3.28.0 DBI1.0.0
[55] ggthemes4.2.0 Rcpp1.0.3 xtable1.8-4
[58] progress1.2.2 htmlTable1.13.2 clue0.3-57
[61] matlab1.0.2 foreign0.8-72 bit1.1-14
[64] km.ci0.5-2 preprocessCore1.48.0 htmlwidgets1.5.1
[67] httr1.4.1 RColorBrewer1.1-2 acepack1.4.1
[70] pkgconfig2.0.3 XML3.98-1.20 R.methodsS31.7.1
[73] nnet7.3-12 dbplyr1.4.2 locfit1.5-9.1
[76] labeling0.3 tidyselect0.2.5 rlang0.4.2
[79] AnnotationDbi1.48.0 munsell0.5.0 tools3.6.1
[82] downloader0.4 generics0.0.2 broom0.5.2
[85] knitr1.25 bit640.9-7 robustbase0.93-5
[88] survMisc0.5.5 purrr0.3.3 EDASeq2.20.0
[91] R.oo1.23.0 xml21.2.2 biomaRt2.42.0
[94] compiler3.6.1 rstudioapi0.10 curl4.2
[97] png0.1-7 ggsignif0.6.0 tibble2.1.3
[100] geneplotter1.64.0 pcaPP1.9-73 stringi1.4.3
[103] GenomicFeatures1.38.0 Matrix1.2-17 KMsurv0.1-5
[106] vctrs0.2.0 lifecycle0.1.0 pillar1.4.2
[109] BiocManager1.30.9 GlobalOptions0.1.1 data.table1.12.6
[112] bitops1.0-6 rtracklayer1.46.0 R62.4.0
[115] latticeExtra0.6-28 hwriter1.3.2 ShortRead1.44.0
[118] gridExtra2.3 codetools0.2-16 assertthat0.2.1
[121] chron2.3-54 openssl1.4.1 rjson0.2.20
[124] withr2.1.2 GenomicAlignments1.22.0 Rsamtools2.2.0
[127] GenomeInfoDbData1.2.2 hms0.5.2 grid3.6.1
[130] rpart4.1-15 tidyr1.0.0 ggpubr0.2.3
[133] base64enc_0.1-3