Last updated: 2018-08-28

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Introduction

Evaluate transcript-level

# Install library

library("tximport")
library("GenomicFeatures")

Loading required package: BiocGenerics

Loading required package: parallel


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

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The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, cbind, colMeans,
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    Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rowMeans, rownames, rowSums, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Loading required package: stats4


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Loading required package: GenomeInfoDb

Loading required package: GenomicRanges

Loading required package: AnnotationDbi

Loading required package: Biobase

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

txdb2 <- makeTxDbFromGFF("/Users/laurenblake/Dropbox/Lauren Blake/Bioinformatics results/gencode.v22.annotation.gtf", format=c("gtf"),
                dataSource="Gencode online",
                organism="Homo sapiens",
                taxonomyId=NA,
                circ_seqs=character(),
                chrominfo=NULL,
                miRBaseBuild=NA,
                metadata=NULL)

Import genomic features from the file as a GRanges object ...

OK

Prepare the 'metadata' data frame ... OK
Make the TxDb object ...

Warning in .get_cds_IDX(type, phase): The "phase" metadata column contains non-NA values for features of
  type stop_codon. This information was ignored.

OK

k <- keys(txdb2, keytype = "TXNAME")
tx2gene <- select(txdb2, k, "GENEID", "TXNAME")

'select()' returned 1:1 mapping between keys and columns

length(unique(tx2gene[,1]))

[1] 198442

length(unique(tx2gene[,2]))

[1] 60483

Awk command to go from annotation file to ENSG and gene name only

cat gencode.v28.annotation.gtf | awk ‘BEGIN{FS=“”}{split($9,a,“;”); if($3~“gene”) print a[1]“”a[3]“”$1“:”$4“-”$5“”$7}’ | sed ‘s/gene_id “//’ | sed ’s/gene_id”//’ | sed ‘s/gene_biotype “//’| sed ’s/gene_name”//’ | sed ’s/“//g’ > Homo_sapiens.GRCh38.92_table.txt

Session information

sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] GenomicFeatures_1.30.3 AnnotationDbi_1.40.0   Biobase_2.38.0        
[4] GenomicRanges_1.30.3   GenomeInfoDb_1.14.0    IRanges_2.12.0        
[7] S4Vectors_0.16.0       BiocGenerics_0.24.0    tximport_1.6.0        

loaded via a namespace (and not attached):
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[11] DBI_1.0.0                  R.utils_2.6.0             
[13] BiocParallel_1.12.0        bit64_0.9-7               
[15] matrixStats_0.54.0         GenomeInfoDbData_1.0.0    
[17] stringr_1.3.1              zlibbioc_1.24.0           
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[23] evaluate_0.11              knitr_1.20                
[25] biomaRt_2.34.2             Rcpp_0.12.18              
[27] backports_1.1.2            DelayedArray_0.4.1        
[29] XVector_0.18.0             bit_1.1-14                
[31] Rsamtools_1.30.0           RMySQL_0.10.15            
[33] hms_0.4.2                  digest_0.6.16             
[35] stringi_1.2.4              rprojroot_1.3-2           
[37] grid_3.4.3                 tools_3.4.3               
[39] bitops_1.0-6               magrittr_1.5              
[41] RCurl_1.95-4.11            RSQLite_2.1.1             
[43] crayon_1.3.4               whisker_0.3-2             
[45] pkgconfig_2.0.2            Matrix_1.2-14             
[47] prettyunits_1.0.2          assertthat_0.2.0          
[49] rmarkdown_1.10             httr_1.3.1                
[51] R6_2.2.2                   GenomicAlignments_1.14.2  
[53] git2r_0.23.0               compiler_3.4.3

This reproducible R Markdown analysis was created with workflowr 1.1.1

Important Transcript-Level Estimates

Lauren Blake

2018-07-13

Introduction

Awk command to go from annotation file to ENSG and gene name only

Session information