Question: The function 'chordDiagramVDJ' from the 'LymphoSeq' Package has 2 code problems
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gravatar for omran.allatif
2.4 years ago by
omran.allatif0 wrote:

Hi,

this post is to report a problem.

The function 'chordDiagramVDJ' from the LymphoSeq Package has 2 code problems.

(I)

When creating the vj data frame (idem dj), with this code :

vj <- sample[, c("vFamilyName", "jFamilyName")]

Both columns of the vj data.frame are Factors, so asking to replace NAs or empty positions by a character string is a wrong code, since the level  "unresolved" doesn't exist.

vj[is.na(vj) | vj == ""] <- "unresolved"

 So the piece of code above must be introduced after the conversion of the vj columns to Character, not before.

 

(II)

When the association =="DJ"

dj <- sample[, c("vFamilyName", "jFamilyName")]

The selected column 'vFamilyName' isn't required, the one required is 'dFamilyName'.

So the wrong code is :

dj <- sample[, c("vFamilyName", "jFamilyName")]

and the correct code is :

dj <- sample[, c("dFamilyName", "jFamilyName")]

 

Best,

Omran

lymphoseq chorddiagramvdj • 287 views
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