Racmacs: a map from scratch using titre data

[kose-bioinfo]

Hi all,

I wanted to see if the small titre table I have is adequate for a simple antigenic map. I have tried making it into a small transposed/and not csv file (UTF-8, comma separated, trimmed spaces) and have gotten a file not supported error. The example file: h3map2004_hitable.csv raises the same error. Checked R version, Racmacs version and dependency versions are up to date. So I'm not sure if it's a simple thing I'm missing or not.

Command:

path_to_titer_file <- system.file("extdata/h3map2004_hitable.csv", package = "Racmacs")
titer_table  <- read.titerTable(path_to_titer_file)

Error:

Error in read.titerTable(path_to_titer_file) : 
  File type '' not supported.

A sample of data I would like to map against a single serum:

Variant1 36.33005722
Variant2 8.482365303
Variant3 0.002970989
Variant4 239.3598926
Variant5 154.5175606
Variant6 28.0855372
Variant7 14.85048931
Variant8 79193.81428
Variant9 3.22E+07

Is it possible to map this data? Are more sera required? is it a simple format issue?

I would greatly appreciate any help.

Thanks

[drserajames]

Hi!

It seems like there are two issues here

1. Reading in data
2. Can you make an antigenic with a single serum?

The answer is 2 is, unfortunately, no. Antigenic cartography turns the titres into distances, so you need quite a few sera to make an antigenic map, at least 4 or 5 distinct sera, and more is better. Otherwise there are not enough constraints to make a consistent map.

The answer to issue 1 is probably not so interesting to you now. I have no problem with the code snippet you posted. It would be helpful to know if you installed Racmacs from CRAN or GitHub, and which operating system you use to see if I can reproduce it.

Thanks,
Sarah

[kose-bioinfo]

Thank you, Sarah! very much appreciated.

I am still interested in your help as I will need to construct some maps in the near future . For Issue 1, my operating system is Ubuntu and I installed the package via CRAN.

install.packages("Racmacs")

I then installed it via github via devtools. Same issue. All my packages seem to be up to date.

Thanks,
Su

[kose-bioinfo]

Hi Sarah,

I wanted to check in and see if there is a solution for the first issue at present, I've since tried with a Windows machine still the same file type error. I've missed something small I'm sure!

[drserajames]

Sorry, I've not seen this error before so I'm not sure what to do. What is the value of path_to_titer_file when you run path_to_titer_file <- system.file("extdata/h3map2004_hitable.csv", package = "Racmacs") ?

[kose-bioinfo]

Thanks, Sarah. I see the problem now, when the data is downloaded and called from the wd it throws up the error. When it's pulled as per your command above it works fine as per the other files in extdata which I can do the mapping fine with. The format must change somehow during the d/l.