brouwern / compbio2021 Goto Github PK

• Ann Wang

Is this chunk of code just changing the class of schrooms_align to AAMultipleAlignment or is it doing something deeper?

I tried to download this, but it did not work. How can I get the HTML to convert to pdf?

since this is not commented out, will it appear in our code? or should this be commented out so that this doesn't show up?

What is the purpose of this line of code?

does anyone know what components to put in the for loop?

I was wondering why the code for renaming the species was only 1 part for homo sapiens but its a lot longer and includes more code for the other species?

(this: shroom_table$spp <- "Homo" VS. shroom_table$spp[grep("laevis",shroom_table$name.orig)] <- "Xenopus")

Hi,
I keep getting this error with entrez_fetch_list

Error: HTTP failure: 500 {"error":"error forwarding request","api-key":"2601:547:500:b8b0:d872:e14f:31db:3a9f","type":"ip", "status":"ok"}

I've got a question about viewing the MSA. Since I've only been able to run it in RStudio Cloud, I'm not sure what the output is supposed to look like. The alignment just appears in my output window, not in a separate plot. How can I fix this?

what does the rep(NA...) function do?

what is the "i" in for(i......) referring to in the line of code? is it just a variable that's always part of a for loop?

here a variable name is separated by '.', everywhere else is with ''. I know both are valid and don't change anything in the long run, but is there a convention you use to distinguish types of variables with how you name them? for example the base variable created uses '' and derivative variables from that use '.'?

To what extent will we need to know for loops for the test?

code by Nathan Brouwer, text by David Hall

What other msa algorithms are commonly used aside from ClustalW and what factors affect which algorithm to use?

"Code by Nathan Brouwer, text by ...."

https://support.bioconductor.org/p/9137290/
^
I was originally having trouble with loading the msa package from Bioconductor, but when I re-downloaded R https://cran.r-project.org/bin/macosx/ from this site using the R.4.1.1.pkg instead of the R.4.1.1.-arm64.pkg it worked!

Code by Nathan Brouwer, text by Hersh

What are the most common ways to change the appearance of your phylogenic trees other than changing the type argument? Going through the help section proved to be overwhelming as there are dozens of different arguments.

I ran the ggmsa function without specifying the package (same with print_msa from compbio4all) and encountered no problem. Just wondering if there is any reason not to do this other than losing specificity about where the function comes from?

can you provide working code for downloading LaTex please

names.focal <- c("XP_392427","EAA12598","ABA81834","XP_783573","CAA78718")

This line appears at line number 734 and I'm confused what names.focal is. Is it an attribute of the names object?

this is a test comment

Code by Nathan Brouwer.
When you say that the fetch function is "cleaning" the data, do you mean that it is consolidating all of the data into smaller groups based on certain categories? Or, is it somehow editing the data into a more understandable format?

In what situations would it be necessary to change the class of an object?

What are the arguments that we should know for the function phylo? In addition, what cases require an unrooted and rooted tree?

Does the msa() function come from the msa package? Or is it from Biostrings or even ggmsa perhaps?

I am trying to knit my code and am getting this error:

processing file: Portfolio1PartA.Rmd
Error in parse_block(g[-1], g[1], params.src, markdown_mode) :
Duplicate chunk label 'setup', which has been used for the chunk:
knitr::opts_chunk$set(echo = TRUE)
Calls: ... process_file -> split_file -> lapply -> FUN -> parse_block
Execution halted

How do I fix this? My code works up to entrez_file_list

Code by Nathan Brouwer, text by Robbie Conner.
Wouldn't this be assigning the amino acid format/template to the current comparisons of the shrooms?

FYI, you can comment out things in the regular text portion of .Rmd file using HTML tags

Are we required to understand this code chunk? If so, can you explain the syntax and what this is doing?

I am getting an error saying,"Error in texi2dvi(texfile, quiet = !verbose, pdf = identical(output, "pdf"), : pdflatex is not available". What does this mean and what do I do to fix it?

I got an Error in texi2dvi saying pdflatex is not available

the package name should be 'compbio4all' currently missing the 'p'