Question: Simulating paths returns identical values
0
gravatar for luke.zappia
15 months ago by
luke.zappia50
luke.zappia50 wrote:

Question received via GitHub https://github.com/Oshlack/splatter/issues/41

I was trying to simulate a differentiation, and followed the instructions for paths in Introduction to Splatter. However, when I then looked at the data with assay(sim.paths), I was greeted by a matrix where all columns (cells) had identical values. Am I doing something wrong? I was hoping to eventually simulate more complex lineage trees.

The code in question:

library(splatter)
sim.paths <- splatSimulate(method = "paths", verbose = FALSE)
sim.paths <- normalise(sim.paths)
View(assay(sim.paths))
splatter • 200 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by luke.zappia50
Answer: Simulating paths returns identical values
0
gravatar for luke.zappia
15 months ago by
luke.zappia50
luke.zappia50 wrote:

When you run View(assay(sim.paths)) you are being shown the first matrix in the assays slot which contains some intermediate values.

To see the counts that have been produced you should use counts(sim.paths) or View(assay(sim.paths, "counts")).

A simple PCA plot coloured by the step along the path can also be helpful plotPCA(sim.paths, colour_by = "Step"). You should be able to see a trend from blue to yellow.

Thanks for giving Splatter a go, hope that helps!

ADD COMMENTlink written 15 months ago by luke.zappia50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 131 users visited in the last hour