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good afternoon and I hope my message finds you well and healthy !! Based on one previous discussion post I had created recently (#735) we would like in a similar way, to expand the analysis in a pan-cancer oriented approach, identifying specific TP53 hotspot mutations amongst specific types of cancer-then, create a merged unified maf object, that contains different cancer samples with only TP53 hotspot mutations, along with respective samples without any T53 mutations, to identify something like "universal co-mutational patterns" , aiming to increase sample size to expand our limited target gene list of co-occurrence mutations; On this premise, my crusial questions are the following:
As mutations are not continuous like gene expression or methylation, merging different maf files would not comprise a "classical" batch effect, correct? And initially I would check at least to merge for example mafs from WES or WGS instead of merging WES with WGS experiments?
In addition, if my approach is valid: based also on my above link: I could apply in each selected cancer separately the step of creating a final maf file with selected TP53 hotspots and not other TP53 mutations-then, the function merge_mafs could be used to merge even for example 4 different mafs? Or it wont work with mafs resulted from different cancers?
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Dear @PoisonAlien ,
good afternoon and I hope my message finds you well and healthy !! Based on one previous discussion post I had created recently (#735) we would like in a similar way, to expand the analysis in a pan-cancer oriented approach, identifying specific TP53 hotspot mutations amongst specific types of cancer-then, create a merged unified maf object, that contains different cancer samples with only TP53 hotspot mutations, along with respective samples without any T53 mutations, to identify something like "universal co-mutational patterns" , aiming to increase sample size to expand our limited target gene list of co-occurrence mutations; On this premise, my crusial questions are the following:
As mutations are not continuous like gene expression or methylation, merging different maf files would not comprise a "classical" batch effect, correct? And initially I would check at least to merge for example mafs from WES or WGS instead of merging WES with WGS experiments?
In addition, if my approach is valid: based also on my above link: I could apply in each selected cancer separately the step of creating a final maf file with selected TP53 hotspots and not other TP53 mutations-then, the function merge_mafs could be used to merge even for example 4 different mafs? Or it wont work with mafs resulted from different cancers?
Thank you in advance,
Efstathios
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