For aminoAcidProperties and related fx: test NAs

Issue #30 resolved
Susanna Marquez
created an issue

Make sure NAs are passed through properly. I.e., an NA appears in the vector instead of a score for the sequence "NA".

Comments (10)

  1. Susanna Marquez reporter

    I think we should make sure NULLs also pass through.

    This behaviour is undesirable, I guess. Given a vector with 4 entries, the function retuns a vector of length 3 with the properties:

    seq_aa_na_null <- c(NA,NULL,"NA","NULL")
     gravy(seq_aa_na, hydropathy =  h)
    [1]   NA 0.27   NA
    
  2. Susanna Marquez reporter

    Should all the property functions return NA in the situation the sequence has invalid characters, or at least don't consider the character in the normalization by length (NULL and NLL should return the same)? It seems some functions that look into the different scales, return NA, but others don't.

    file <- system.file("extdata", "changeo_demo.gz", package="alakazam")
    db <- readChangeoDb(file)
    db[1,"JUNCTION"] <- NA
    db[2,"JUNCTION"] <- "NA"
    db[3,"JUNCTION"] <- "NULL"
    db[4,"JUNCTION"] <- "NLL"
    junction_properties_na <- aminoAcidProperties(db[1:4,], seq="JUNCTION", nt=FALSE,
                                                  trim=FALSE, label="JUNCTION",
                                                  hydropathy = h)
    junction_properties_na[,grep("_AA_",colnames(junction_properties_na))]
    
      JUNCTION_AA_LENGTH JUNCTION_AA_GRAVY JUNCTION_AA_BULK
    1                 NA                NA               NA
    2                  2         0.2700000            12.16
    3                  4                NA               NA
    4                  3        -0.4633333            18.54
      JUNCTION_AA_ALIPHATIC JUNCTION_AA_POLARITY
    1                    NA                   NA
    2                  0.50             9.850000
    3                  1.95                   NA
    4                  2.60             7.133333
      JUNCTION_AA_CHARGE JUNCTION_AA_BASIC JUNCTION_AA_ACIDIC
    1                 NA                NA                 NA
    2                  0                 0                  0
    3                  0                 0                  0
    4                  0                 0                  0
      JUNCTION_AA_AROMATIC
    1                   NA
    2                    0
    3                    0
    4                    0
    
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