How to run script in several data frames at once?

Question

I have 58 data named as: h5, h6,... h64. I want to run following script on all of them at one time and save the result in 1 new data file. this is my script:

t <- read.table("h5",header = F, row.names=1)
 cor(t)
 (cor(t))^2
lm(t$V3 ~ t$V2, data=t)

I know for reading all the data files at once I can use :

myFiles <- list.files(pattern="h.*")

But for the rest I do not know how to make a loop or how to store the result in a new data frame. any suggestion?

I show in below my input file structure :

HO840M3000540481 993.38 1543.1765
HO840M3000540483 -0.51 1120.8224
HO840M3000540497 1192.06 1651.3322
HO840M3004672697 388.5 1140.0917
HO840M3004672704 426.9 836.3676
HO840M3006005895 524.65 1301.8218
HO840M3006972816 1673.99 1389.1919
HO840M3006988837 188.35 385.6415
HO840M3006988891 2987.58 1919.2762
HO840M3006989113 1097.59 1746.4724
HO840M3007701817 1320.5 1058.4915
HO840M3007701858 -372.15 1090.6167
HO840M3007815980 548.58 759.3870

you can either check the total row count first and create an empty data.frame which you fill on each iteration or write/reload to a table with append write.table(x, file = "", append = TRUE) — timfaber
– timfaber, Commented Apr 13, 2017 at 6:18

Adam Quek · Accepted Answer · 2017-04-13 07:52:37Z

1

Here's a shot in the dark...

myFiles <- paste0("h", 5:64)
all <- lapply(myFiles, read.table, header=F, row.names=1)

t1 <- lapply(all, cor)
t2 <- lapply(all, function(x) (cor(x))^2)

all.lm <- lapply(all, function(x)lm(V3 ~ V2, data=x))

EDIT: I can't reproduce the error mentioned in the comment, based on the data-structure provided. See below for the execution.

Please elaborate on what specific error you are facing.

dat <- structure(list(V2 = c(993.38, -0.51, 1192.06, 388.5, 426.9, 524.65, 
1673.99, 188.35, 2987.58, 1097.59, 1320.5, -372.15, 548.58), 
V3 = c(1543.1765, 1120.8224, 1651.3322, 1140.0917, 836.3676, 
1301.8218, 1389.1919, 385.6415, 1919.2762, 1746.4724, 1058.4915, 
1090.6167, 759.387)), .Names = c("V2", "V3"), class = "data.frame", row.names = c("HO840M3000540481", 
"HO840M3000540483", "HO840M3000540497", "HO840M3004672697", "HO840M3004672704", 
"HO840M3006005895", "HO840M3006972816", "HO840M3006988837", "HO840M3006988891", 
"HO840M3006989113", "HO840M3007701817", "HO840M3007701858", "HO840M3007815980"
))

all <- list(dat)


lapply(all, cor)


[[1]]
          V2        V3
V2 1.0000000 0.6741098
V3 0.6741098 1.0000000

lapply(all, function(x) (cor(x))^2)

[[1]]
          V2        V3
V2 1.0000000 0.4544241
V3 0.4544241 1.0000000


lapply(all, function(x)lm(V3 ~ V2, data=x))

[[1]]

Call:
lm(formula = V3 ~ V2, data = x)

Coefficients:
(Intercept)           V2  
   943.3531       0.3354

edited Apr 13, 2017 at 7:52

answered Apr 13, 2017 at 6:22

Adam Quek

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9 Comments

zara Over a year ago

I get this error:Error in FUN(X[[i]], ...) : no lines available in input

Adam Quek Over a year ago

Can't help you without knowing what your data structure is.

zara Over a year ago

i put a part of data in my explanation to show you how is the data structure. meanwhile I do not have h17 and h33

zara Over a year ago

thanks, but again the same error: all <- lapply(myFiles, read.table, header=F, row.names=1) Error in FUN(X[[i]], ...) : no lines available in input

Adam Quek Over a year ago

Check your file names with list.files. Make sure the file name, path and extension are all correctly stated.

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