Slicing function does not work

[JulianRozenberg]

Hello

Slicing function returns an error suggesting that the region is missing when it is not,

Sincerely.

Julian Rozenberg

slicing("df80679e-c4d3-487b-934c-fcc782e5d46e",

• regions="chr17:75000000-76000000", token = GDC_TOKEN, overwright == TRUE) Error in slicing("df80679e-c4d3-487b-934c-fcc782e5d46e", regions = "chr17:75000000-76000000", : missing(regions) || missing(symbols) is not TRUE

[LiNk-NY]

Hi @JulianRozenberg There is a typo that is causing this error that you are seeing.

> missing(regions) || missing(symbols) 
Error: object 'overwright' not found

Can you try:

slicing("df80679e-c4d3-487b-934c-fcc782e5d46e",
    regions="chr17:75000000-76000000", token = GDC_TOKEN, overwrite = TRUE)

Best, Marcel

[JulianRozenberg]

Hi Marcel! Thank you very much for you comment, Unfortunately not the case. fnames = lapply(Bam_filter, slicing, overwrite = TRUE, regions="chr15:75353745-75353745",token == gdc_token()) or

slicing(uuid=Bam_filter[1], regions = "chr15:75353745-75353745", destination = file.path("/home/jrozenberg/Variantcalling/TCGA/SlicedBAMS_1.8.22",paste0(uuid, ".bam")), overwrite = TRUE, progress = interactive(), token == gdc_token(), legacy = FALSE ) Again , thank you for you help only, I am not completely sure how to specify token in R (I am just learning it) such as GDC_TOKEN <- "xy..."

[LiNk-NY]

Hi Julian, @JulianRozenberg

You still have a double == in the code. Please make it, e.g., token = gdc_token(). You also need dbGap access to use the gdc_token() so make sure you have that.

Best regards, Marcel

[JulianRozenberg]

Aha, This made it. fnames = lapply(Bam_filter, slicing, overwrite = TRUE, regions="chr17:42614538-42614738",token = GDC_TOKEN) Thank you very much for you help, Julian

On Tue, Aug 2, 2022 at 4:47 PM Marcel Ramos @.***> wrote:

Hi Julian, @JulianRozenberg https://github.com/JulianRozenberg

You still have a double == in the code. Please make it, e.g., token = gdc_token(). You also need dbGap access to use the gdc_token() so make sure you have that.

Best regards, Marcel

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