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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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X and Y chromosome missing in 'infercnv.png' #525

Open wlc9355 opened 1 year ago

wlc9355 commented 1 year ago

Hi, After using this user-friendly R tool, the 'infercnv.png' was output. However, I found there was no image information about X and Y chromosome. How could I solve this problem? Parameter adjustment, input data adjustment or others? Looking forward to your kind anwser. Many thanks!

Best wishes, LC Wei

infercnv

GeorgescuC commented 1 year ago

Hi @wlc9355 ,

By default, those chromosomes are filtered out because there are other factors than CNVs that could be affecting the signal. This behavior is controlled by the chr_exclude=c('chrX', 'chrY', 'chrM') option in the CreateInfercnvObject() method.

Regards, Christophe.

astaburuaga-garcia commented 1 year ago

Hi, then how should I specify that I don't want to exclude anything? chr_exclude = NULL ?

GeorgescuC commented 1 year ago

Hi @astaburuaga-garcia ,

Yes, using chr_exclude=NULL works. You can also use chr_exclude=c().

Regards, Christophe.