读取特定行的大型矩阵数据文件 [英] Reading specific rows of large matrix data file
问题描述
假设我有一个巨大的m * n矩阵 X （太大而无法读入内存）和二进制数字向量 V 长度 m 。我的目标是读取 X 的行，对应 V 等于 1 （而不是与 V [i] == 0 对应的那些）进入专用的数据表 / 矩阵通过包，例如（但不一定相同） bigmemory 或 FF 。仅对应于 V [i] == 1 的行。
Suppose I have a gigantic m*n matrix X (that is too big to read into memory) and binary numeric vector V with length m. My objective is to read the rows of X that correspond to V equalling 1 (and not those corresponding to V[i] == 0) into a dedicated data table/matrix through a package such as (but not necessarily identical to) bigmemory or ff. only for the rows corresponding to V[i] == 1.
这可以通过黑客攻击来实现c $ c> nrows 和跳过等等 read.table 但是我我正在寻找 bigmemory ， ff 等。因RAM不足而输入类型解决方案。
This can be done by hacking nrows and skip and so on in read.table but I'm looking for a bigmemory, ff et al. type solution due to insufficient RAM.
这是一个MWE，它不能反映我的 X 的实际大小。
Here's a MWE that does not reflect the true size of my X.
X <- array(rnorm(100*5),dim=c(100,5))
write.csv(X,"target.csv")
V <- sample(c(rep(1,50),rep(0,50))) #Only want to read in half the rows corresponding to 1's
rm(X)
#Now ... How to read "target.csv"?
推荐答案
如何使用命令行工具 sed ，构造一个命令，传递你想在命令中读取的行。我不确定是否会对此有一些命令长度限制...
How about you use the command line tool sed, constructing a command that passes along the lines you want to read in the command. I am not sure if there would be some command length limit on this...
# Check the data
head( X )
# [,1] [,2] [,3] [,4] [,5]
#[1,] 0.2588798 0.42229528 0.4469073 1.0684309 1.35519389
#[2,] 1.0267562 0.80299223 -0.2768111 -0.7017247 -0.06575137
#[3,] 1.0110365 -0.36998260 -0.8543176 1.6237827 -1.33320291
#[4,] 1.5968757 2.13831188 0.6978655 -0.5697239 -1.53799156
#[5,] 0.1284392 0.55596342 0.6919573 0.6558735 -1.69494827
#[6,] -0.2406540 -0.04807381 -1.1265165 -0.9917737 0.31186670
# Check V, note row 6 above should be skipped according to this....
head(V)
# [1] 1 1 1 1 1 0
# Get line numbers we want to read
head( which( V == 1 ) )
# [1] 1 2 3 4 5 7
# Read the first 5 lines where V == '1' in your example (remembering to include an extra line for the header row, hence the +1 in 'which()')
read.csv( pipe( paste0("sed -n '" , paste0( c( 1 , which( V == 1 )[1:6] + 1 ) , collapse = "p; " ) , "p' C:/Data/target.csv" , collapse = "" ) ) , head=TRUE)
# X V1 V2 V3 V4 V5
#1 1 0.2588798 0.4222953 0.4469073 1.0684309 1.35519389
#2 2 1.0267562 0.8029922 -0.2768111 -0.7017247 -0.06575137
#3 3 1.0110365 -0.3699826 -0.8543176 1.6237827 -1.33320291
#4 4 1.5968757 2.1383119 0.6978655 -0.5697239 -1.53799156
#5 5 0.1284392 0.5559634 0.6919573 0.6558735 -1.69494827
#6 7 0.6856038 0.1082029 0.1523561 -1.4147429 -0.64041290
我们实际传递给 sed 的命令是......
The command we are actually passing to sed is...
"sed -n '1p; 2p; 3p; 4p; 5p; 6p; 8p' C:/Data/target.csv"
我们使用 -n 关闭任何行的打印，然后我们使用一个分号分隔的行号，我们想读取这些行号，由给我们（V == 1），最后是目标文件名。记住这些行号已被 +1 抵消，以说明组成标题行的行。
We use -n to turn off printing of any lines, and then we use a semi-colon separated vector of lines numbers that we do want to read, given to us by which( V == 1 ), and finally the target filename. Remember these line numbers have been offset by +1 to account for the line that makes up the header row.
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