一切按照教程使用该代码
D:\ICGC_PACA_CA>Rscript ICGC_DataProcess.r -h
Warning message:
'argparser'R3.6.2
usage: ICGC_DataProcess.r [--] [--help] [--opts OPTS] [--fmt1 FMT1]
[--fmt2 FMT2] [--exp_file EXP_FILE] [--clinical_file
CLINICAL_FILE] [--output_file1 OUTPUT_FILE1] [--output_file2
OUTPUT_FILE2] [--mart MART] [--dataset DATASET] [--gender1
GENDER1] [--gender2 GENDER2] [--os1 OS1] [--os2 OS2] [--fun FUN]
ICGC data preprocessing
flags:
-h, --help show this help message and exit
optional arguments:
-x, --opts RDS file containing argument values
-f, --fmt1 data file format [default: tsv]
--fmt2 data file format [default: tsv]
-e, --exp_file gene expression file
-c, --clinical_file clinical file
-o, --output_file1 output exp file
--output_file2 output clinical file
-m, --mart useMart database [default: ENSEMBL_MART_ENSEMBL]
-d, --dataset useDataset [default: hsapiens_gene_ensembl]
-g, --gender1 male [default: 1]
--gender2 female [default: 0]
--os1 vital status [default: 0]
--os2 vital status [default: 1]
--fun function [default: mean]
D:\ICGC_PACA_CA>Rscript ICGC_DataProcess.r --fmt1 tsv --fmt2 tsv --exp_file exp_seq.PACA-CA.tsv --clinical_file donor.PACA-CA.tsv --out
put_file1 sample_exp_file.txt --output_file2 sample_clinical_file.txt --mart ENSEMBL_MART_ENSEMBL --dataset hsapiens_gene_ensembl --gen
der1 1 --gender2 0 --os1 0 --os2 1 --fun mean
Warning message:
'argparser'R3.6.2
Error in apply(large_exp_2[, -1], 2, as.numeric) :
dim(X) must have a positive length
Calls: aggregate -> as.data.frame -> apply
多谢尝试后均是在dim(X) must have a positive length初出现错误，求各位大神帮忙看看，感激不尽
