Problem with ribosomal = TRUE

[nramme]

Hello, I'm trying to calculate CU for ribosomal genes, but it only shows "self".

milc <- MILC(FIF10_cod, ribosomal = TRUE)

head(milc)

self
[1,] 0.6694753
[2,] 0.5570909
[3,] 0.5825481
[4,] 0.6805010
[5,] 0.5265362
[6,] 0.5162219

Here's my input:

>Cg_02C|definition|ribosomal protein S8 CDS ATGGGAGTAAACCACAGAGGAGAGCACAAGCGCAGAAAGACTGGAGCAAAGGCAGTGATTTCACGCAAGAAGAGGAACAAC >Cg_03|definition|hypothetical protein CDS ATGGGCGGATGTGATGCAGTGCTGAGGATCTTTGAAGTGACTGGGAATTCGTTTGTTGTTGGAGGCATAAGTGTGCTTGTAAG >Cg_06A|definition|ribosomal protein L5 CDS ATGAGTAGCGCAAAGGGAACACGATCGTACAGCACCAACTTCCAAGTGAAGAGAAGGAGGAGGAGAGAGGGAAAGACTGAC

What am I doing wrong? Thanks.

[nick-youngblut]

I'm struggling with this too. It's not clear from the docs how ribosomal genes are identified when ribosomal = TRUE. Is it based on KO, raw annotation strings, or something else?

From the docs:

If the sequences in the set are annotated, we can choose to calculate CU bias with respect to codon usage of ribosomal genes (i.e. codon usage of the subset of sequences in the sample which are annotated as ribosomal genes) simply by setting ribosomal = TRUE

...but "annotated" is very vague

[nick-youngblut]

Based on the code, ribosomal = TRUE is based on KOs:

        if (ribosomal) {
            ribKOs <- cTobject@KO %in% RPKOs
            if (any(ribKOs))
                subsets <- c(list(ribosomal = ribKOs), subsets)
        }

The "ribosomal" KOs:

RPKOs <- c(
    "K02945","K02967","K02982","K02986","K02988","K02990","K02992","K02994",
    "K02996","K02946","K02948","K02950","K02952","K02954","K02956","K02959",
    "K02961","K02963","K02965","K02968","K02970","K02981","K02985","K02984",
    "K02987","K02989","K02991","K02993","K02995","K02997","K02947","K02949",
    "K02951","K02953","K02955","K02958","K02957","K02960","K02962","K02964",
    "K02966","K02969","K02971","K02973","K02974","K02975","K02976","K02978",
    "K02977","K02979","K02980","K02983","K02998","K02863","K02886","K02906",
    "K02926","K02931","K02933","K02935","K02939","K02864","K02867","K02869",
    "K02871","K02874","K02876","K02878","K02879","K02881","K02884","K02887",
    "K02888","K02890","K02892","K02895","K02897","K02899","K02902","K02904",
    "K02907","K02909","K02911","K02913","K02914","K02916","K02919","K07590",
    "K02925","K02930","K02932","K02934","K02937","K02936","K02938","K02940",
    "K02866","K02865","K02868","K02870","K02873","K02872","K02875","K02877",
    "K02880","K02883","K02882","K02885","K02889","K02891","K02894","K02893",
    "K02896","K02898","K02901","K02900","K02903","K02905","K02908","K02910",
    "K02912","K02915","K02918","K02917","K02920","K02922","K02921","K02923",
    "K02924","K02927","K02928","K02929","K02941","K02942","K02943","K02944",
    "K01977","K01980","K01985","K01979","K01982","K01981"
)

[sakuragi0109]

Hi, I used Prokka for my annotation, so I don't have KO ID for my file, and I cannot get ribosomal calculation either. What should I do?