Doing dist on separate objects in a text file
On Nov 5, 2011, at 7:20 PM, ScottDaniel wrote:
So I have a text file that looks like this: "Label" "X" "Y" "Slice" 1 "Field_1_R3D_D3D_PRJ_w617.tif" 348 506 1 2 "Field_1_R3D_D3D_PRJ_w617.tif" 359 505 1 3 "Field_1_R3D_D3D_PRJ_w617.tif" 356 524 1 4 "Field_1_R3D_D3D_PRJ_w617.tif" 2 0 1 5 "Field_1_R3D_D3D_PRJ_w617.tif" 412 872 1 6 "Field_1_R3D_D3D_PRJ_w617.tif" 422 863 1 7 "Field_1_R3D_D3D_PRJ_w617.tif" 429 858 1 8 "Field_1_R3D_D3D_PRJ_w617.tif" 429 880 1 9 "Field_1_R3D_D3D_PRJ_w617.tif" 437 865 1 10 "Field_1_R3D_D3D_PRJ_w617.tif" 447 855 1 11 "Field_1_R3D_D3D_PRJ_w617.tif" 450 868 1 12 "Field_1_R3D_D3D_PRJ_w617.tif" 447 875 1 13 "Field_1_R3D_D3D_PRJ_w617.tif" 439 885 1 14 "Field_1_R3D_D3D_PRJ_w617.tif" 2 8 1 What it represents are the locations of centromeres per nucleus in a microscope image. What I need to do is do a dist() on each grouping (the grouping being separated by the low values of x and y's) and then compute an average. The part that I'm having trouble with is writing code that will allow R to separate these objects.
I'm having trouble figuring out what you mean by "separating the objects". Each row is a separate reading, and I think you just want pairwise distances, right?
Do I have to find some way of creating separate data frames for each object?
I don't think so. You need to read this file into a data.frame which should be fairly trivial with read.table is you specify the header=TRUE parameter.
Or is there a way to parse the file and generate a single data frame of all the pairwise distances?
Then assuming there is now a data.frame named "dat" with those values:
dist( cbind(dat$X, dat$Y))
One stumbling block might have been recognizing that the dist function
will not work with two x and y arguments but rather requires a matrix
(or something coercible to a matrix) as its first argument. This
would also have worked:
dist(dat[ , c("X", "Y")])
David. > Any > suggestions or example code would be much appreciated. Thanks! > > -- > View this message in context: http://r.789695.n4.nabble.com/Doing-dist-on-separate-objects-in-a-text-file-tp3994515p3994515.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT