gisticChromPlot for individual samples

[MaryGoAround]

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
gistic_s1@cnv.summary <- gistic_s1@cnv.summary[gistic_s1@cnv.summary$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
gistic_s1@gis.scores <- gistic_s1@gis.scores[gistic_s1@gis.scores$Tumor_Sample_Barcode == "s1", ]

# Filter @cytoband.summary slot
gistic_s1@cytoband.summary <- gistic_s1@cytoband.summary[gistic_s1@cytoband.summary$Tumor_Sample_Barcode == "s1", ]

# Filter @gene.summary slot
gistic_s1@gene.summary <- gistic_s1@gene.summary[gistic_s1@gene.summary$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

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