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!
--
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