- The error “Error in library() : there is no package called “”
indicates that the package is not installed. Rerun the code listed
in the materials section of the protocol. - The user must enter their working directory file path name
where the R code prompts “enter file path here.” - The error “Error: could not find function” indicates that the
library has not been installed or loaded. Rerun the code listed
in the materials section of the protocol or the first step of the
methods to install and load the package. - The error “Error in .Call2("new_input_filexp", filepath,
PACKAGE¼"XVector") : cannot open file ’Human_Pro-
teome.fa.gz ’” indicates that the Human_Proteome.fa.gz file
is not located in your working directory. Change your working
directory to the location of the file. - The final Excel sheet produced by the R script is saved in the
user’s working directory. This can be found by typing “getwd
()” at the console in RStudio. To list the files in your working
directory from R, type “dir()” at the console in RStudio. To
change the user’s working directory, navigate in the header in
RStudio to Session!Set Working Directory!Choose Direc-
tory, and then select the desired location of the working direc-
tory. Alternatively, enter the following code at the console in
RStudio: setwd("Path to directory"). - This protocol results in the identification of 44,762 proteins.
Putative target selection is dependent on the interest of the
researcher. Further stratification can be accomplished by asses-
sing species conservation. This can be accomplished by rerun-
ning the script using a FASTA file containing protein sequences
from a different species. Additionally, conducting gene ontol-
ogy analysis (GO) may be used to further characterize putative
targets. To accomplish this, the investigator may download
additional annotation information such as Gene Ontology
from biomaRT (https://www.bioconductor.org/packages/
release/bioc/html/biomaRt.html). To list available annota-
tion information and download GO identifiers, the researcher
may replace the following code instep 11of Subheading3.1:
Keys<- accession$ensembl_peptide_id
mymarthuman<- useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
mymarthuman<-
useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",
host="www.ensembl.org")
listAttributes(mymarthuman)
myhitshuman_genename<- getBM(attributes=c("ensembl_peptide_id", "external_gene_name",
"go_id", "definition_1006"), values = Keys, mart = mymarthuman)
Identification and Validation of Novel Targets 107