用maftools分析GISTIC文件报错
我用了两种方法做GISTIC,分别在不同的地方报错,有没有大神可以帮忙解决一下
方法一:从TCGA官网下载文件后在GISTIC在线平台分析
在读取GISTIC文件处报错
代码如下:
rm(list = ls())
options(stringsAsFactors = F)
library(maftools)
laml.gistic = readGistic(gisticAllLesionsFile = 'C:/Users/Meredith/Desktop/maftools/all_lesions.conf_90.txt',
gisticAmpGenesFile = 'C:/Users/Meredith/Desktop/maftools/amp_genes.conf_90.txt',
gisticDelGenesFile = 'C:/Users/Meredith/Desktop/maftools/del_genes.conf_90.txt',
gisticScoresFile = 'C:/Users/Meredith/Desktop/maftools/scores.gistic',
isTCGA = TRUE)
#结果报错
>Error in `levels<-`(`*tmp*`, value = as.character(levels)) :
factor level [61] is duplicated
方法二:在firehose直接下载GISTIC分析结果
在生成图片处报错
代码如下:
plotCBSsegments(cbsFile = 'C:/Users/Meredith/Desktop/maftools/BLCA.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt' )
#结果报错
>Error in rep(chr.colors, seg.spl.transformed[, .N, Chromosome][, N]) :
'times'参数不对