使用ICGC数据库进行肿瘤组织突变分析,绘制瀑布图等
weixin_56804090:
您好,在运行a waterfall(inputMatrix,fileType = "Custom",variant_class_order = levels(factor(inputMatrix$variant_class)),mainPalette = rainbow(22),plotGenes = genes_family)
Checking if input is properly formatted...
Detected "Custom" file_type flag, looking for correct column names...
Calculating frequency of mutations...
Removing genes not in: PRMT1, PRMT2, PRMT3, CARM1, PRMT5, PRMT6, PRMT7, PRMT8, PRMT9
setting mutation hierarchy...
NULL
Warning messages:
1: In waterfall_Custom2anno(x, label_col) :
Did not detect silent mutations in input, is this expected?
2: In data.table::melt(mutation_counts) :
The melt generic in data.table has been passed a table and will attempt to redirect to the relevant reshape2 method; please note that reshape2 is deprecated, and this redirection is now deprecated as well. To continue using melt methods from reshape2 while both libraries are attached等,不知道怎么解决。
TCGA的差异分析(limma和edgeR)
酒732:
我的logFC全部都是正的,咋办呢,是不是哪出错了
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