我想使用/改变obs我在 data.table 中创建的列，但返回错误
Error in eval(jsub, SDenv, parent.frame()) : object 'obs' not found
请参阅示例数据的实现。
library(data.table)
set.seed(0)
dt <- data.table(
index = sample(0:100, 10, replace=FALSE),
value = 1:100)
dt[, `:=`(obs = seq_along(index)-1, window = floor(obs/10))] #create an index of every observation and bin them
读取大文件 ~335GB 时 fread() 失败并出现此错误。感谢任何有关如何解决此问题的建议。
opt$input_file <- "sample-009_T/per_read_modified_base_calls.txt"
Error in data.table::fread(opt$input_file, nThread = 16) :
long vectors not supported yet: ../../src/include/Rinlinedfuns.h:537
Execution halted
文件大小和片段
(base) bash-4.2$ ls -thl per_read_modified_base_calls.txt
-rw-r--r-- 1 lih7 user 335G May 31 15:24 per_read_modified_base_calls.txt
(base) bash-4.2$ head per_read_modified_base_calls.txt
read_id chrm strand pos mod_log_prob can_log_prob mod_base
d1c2a9e7-8655-4393-8ab1-c1fa47b0dc5c chr12 + 94372964 -8.814943313598633 -8.695793370588385 h
d1c2a9e7-8655-4393-8ab1-c1fa47b0dc5c chr12 + 94372964 -0.00031583529198542237 -8.695793370588385 m
2109b127-c835-47f3-b215-c238438829b6 chr10 - 118929450 -3.0660934448242188 -5.948376270726361 h
2109b127-c835-47f3-b215-c238438829b6 chr10 - 118929450 -0.05046514421701431 -5.948376270726361 m
2109b127-c835-47f3-b215-c238438829b6 chr10 - …我有包含两组的数据数据框：肿瘤组和正常组。对于每个站点/行，我想计算费舍尔精确值以用于Methyl UnMethy之间的使用Tumor and Normal
我正在寻找如何使用 dplyr 方法转换数据以计算每个站点的渔民精确度。
methyl_dat <- data.frame(loci = c("site1", "site2", "site3", "site4"),
Methy.tumor = c(50, 5, 60, 12),
UnMethy.tumor = c(60, 0, 65, 5),
Methy.Normal = c(13, 5, 22, 3),
UnMethy.Normal = c(86, 0, 35, 3) )
这是 Fischer 对站点 1 的精确策略
Normal
Tumor Methyl UnMethy
Methy 50 13
UnMethy 60 86