anpefi / msap Goto Github PK

This is a suggestion by Juan Cesar Vilardi.

Una sería que en el manual del paquete se recomendara el uso de la
función sink() (de manera similar a lo que indico más abajo)

sink("msap.txt")
msap("ejemplo.csv",name="ejemplo", do.pairwisePhiST=TRUE)
sink()

Esto es importante cuando se trabaja con Rstudio, dado que en el
.Rhistory con se incluyen las salidas.

As requested by Rik Lievers, it could be interesting a quick plot to check the Mantel test.

Currently, there are a hard threshold of at least two occurrences of each state to define a MSL or NML as polymorphic. This was settled following Herrera & Bazaga 2010, but some users (Massimiliano Lauria the most recent) suggested that they want consider another thresholds. So it would be desirable to allow the users to decide this threshold, independently for each type of marker.

From a mail from He Zinqing:

The origin MSAP protocol uses isoesquizomeric endonucleases HpaII and MspI, but I use Tfi I/Pfe I in our study according to the paper Stable Epigenetic Variants Selected from an Induced Hypomethylated Fragaria vesca Population (Jihua Xu et al. 2016, in the attachment). So in our study, Tfi I/Pfe patterns are: (1/1: unmethylation; 1/0: hemimethylation; 0/0: methylation; 0/1: missing data). It is different from HPA/MSP patterns, so we can’t use R package msap.

This a thing to study and it would be a great addition

When running any analysis now the pairwise PhiST yield the following error:

Error in FUN(X[[i]], ...) : 'bin' must be numeric or a factor

Perhaps it is because a dependency (see #3 )

This is a suggestion by Juan Cesar Vilardi

La otra sugerencia sería que la sección de los phist de a pares se
simplificara de manera que se pudiera exportar más fácilmente a una
planilla de cálculo (haciendo corte y pega)

Pair Phi_ST P

A1-A120 0.1859 0.002
A1-A24 0.1169 0.0015

as suggested by Jekayinoluwa, Temitope

Reported originally by Jimena Cascales:
Error in inherits(m2, "dist") : object 'DM.NML' not found

This happens when do.cluster=F and do.mantel=F because DM.NML is wrongly assigned inside the cluster routine.

Currently, msap is assuming that dataset has not any missing value. But if there are missing data for a band but not for the other in the Hpa/Msp pair, the combined would assume that the missing value is 0 (no. band) without any warning.

https://r-forge.r-project.org/tracker/index.php?func=detail&aid=6262&group_id=1422&atid=5292

This is the issue #6262 in the R-Forge support tracker

Original comment in R-Forge:

Anonymous message posted by [email protected]

I had been running msap successfully with my dataset. I then reduced the number of loci in the dataset (after some data clean up) and now I am getting the following error:

Error in nj(DM_copy) :
missing values are not allowed in the distance matrix
Consider using njs()

I edited the source code to use njs() but I'm now left with an error that causes my PCoA plotting to fail:

Error in cmdscale(DM, k = length(inds) - 1, eig = T) :
NA values not allowed in 'd'

I am assuming that there are values in my distance matrix that don't exist possibly due to the reduction in the size of my data set? Do you have some advice that might help me remedy this problem? I've attached the data file I am running.

Thanks!