## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set( collapse=TRUE, comment="#>", warning=FALSE, error=FALSE, eval=TRUE ) ## ----library, message=FALSE, warning=FALSE, error=FALSE----------------------- library(BiocStyle) library(HPAanalyze) library(dplyr) ## ----------------------------------------------------------------------------- CCNB1xml <- hpaXmlGet("ENSG00000134057") CCNB1_ab <- hpaXmlAntibody(CCNB1xml) CCNB1_ab #> # A tibble: 4 x 4 #> id releaseDate releaseVersion RRID #> #> 1 CAB000115 2006-03-13 1.2 #> 2 CAB003804 2006-10-30 2 AB_562272 #> 3 HPA030741 2013-12-05 12 AB_2673586 #> 4 HPA061448 2016-12-04 16 AB_2684522 CCNB1_expr <- hpaXmlTissueExpr(CCNB1xml) str(CCNB1_expr[[1]]) #> Classes 'tbl_df', 'tbl' and 'data.frame': 331 obs. of 18 variables: #> $ patientId : chr "1653" "1721" "1725" "598" ... #> $ age : chr "53" "60" "57" "7" ... #> $ sex : chr "Male" "Female" "Male" "Male" ... #> $ staining : chr NA NA NA NA ... #> $ intensity : chr NA NA NA NA ... #> $ quantity : chr NA NA NA NA ... #> $ location : chr NA NA NA NA ... #> $ imageUrl : chr "http://v18.proteinatlas.org/images/115/2043_B_4_5.jpg" "http://v18.proteinatlas.org/images/115/2043_B_6_5.jpg" "http://v18.proteinatlas.org/images/115/2043_B_5_5.jpg" "http://v18.proteinatlas.org/images/115/2043_A_2_2.jpg" ... #> $ snomedCode1 : chr "M-00100" "M-00100" "M-00100" "M-00100" ... #> $ snomedCode2 : chr "T-93000" "T-93000" "T-93000" "T-66000" ... #> $ snomedCode3 : chr NA NA NA NA ... #> $ snomedCode4 : chr NA NA NA NA ... #> $ snomedCode5 : chr NA NA NA NA ... #> $ tissueDescription1: chr "Normal tissue, NOS" "Normal tissue, NOS" "Normal tissue, NOS" "Normal tissue, NOS" ... #> $ tissueDescription2: chr "Adrenal gland" "Adrenal gland" "Adrenal gland" "Appendix" ... #> $ tissueDescription3: chr NA NA NA NA ... #> $ tissueDescription4: chr NA NA NA NA ... #> $ tissueDescription5: chr NA NA NA NA ... ## ----eval=FALSE--------------------------------------------------------------- # dir.create("img") # for (i in 1:nrow(CCNB1_expr[[1]])) { # download.file(CCNB1_expr[[1]]$imageUrl[i], # destfile = paste0("img/", CCNB1_ab$id[1], "_", # CCNB1_expr[[1]]$patientId[i], "_", # CCNB1_expr[[1]]$tissueDescription2[i], # ".jpg"), # mode = "wb") # }