Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

gisticChromPlot for individual samples #1038

Closed
MaryGoAround opened this issue Jul 12, 2024 · 2 comments
Closed

gisticChromPlot for individual samples #1038

MaryGoAround opened this issue Jul 12, 2024 · 2 comments
Labels

Comments

@MaryGoAround
Copy link

Hi I need your help please

I have created a gistic object for ten samples but I only want to run gisticChromPlot for each sample I then tried to subset whole gistic object per samples as below

gistic_s1 <- gistic_object
gistic_s1@data <- gistic_s1@data[gistic_s1@data$Tumor_Sample_Barcode == "s1", ]

# Filter @cnv.summary slot
[email protected] <- [email protected][[email protected]$Tumor_Sample_Barcode == "s1", ]

# Filter @numericMatrix slot
gistic_s1@numericMatrix <- gistic_s1@numericMatrix[, "s1", drop = FALSE]

# Filter @cnMatrix slot
gistic_s1@cnMatrix <- gistic_s1@cnMatrix[, "s1", drop = FALSE]

# Filter @gis.scores slot
[email protected] <- [email protected][[email protected]$Tumor_Sample_Barcode == "s1", ]

# Filter @cytoband.summary slot
[email protected] <- [email protected][[email protected]$Tumor_Sample_Barcode == "s1", ]

# Filter @gene.summary slot
[email protected] <- [email protected][[email protected]$Tumor_Sample_Barcode == "s1", ]

# Plot the filtered GISTIC object
gisticChromPlot(gistic = gistic_s1, markBands = "all")

Error in strsplit(x = g$loc, split = "-") : non-character argument

which gives error I guess because gistic.score slot for subsetted object is empty

Please do you have any idea to visualise gistic results per sample (amplified/deleted peaks)

Thanks for any help
Rplot01

Copy link

This issue is stale because it has been open for 60 days with no activity.

@github-actions github-actions bot added the stale label Sep 11, 2024
Copy link

This issue was closed because it has been inactive for 14 days since being marked as stale.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant