Remove rows in an array containing a non-matching element

I have a datafile data.txt:

gene12 489 483 838
gene82 488 763 920
gene31 974 837 198
gene45 489 101 378
gene59 89 827 138

I have another data file genelist.txt that lists just genes I'm interested in for my study:

gene45
gene59
gene61

I want to modify the first dataset by removing all rows where the gene isn't found in the second list so basically end up with this array:

gene45 489 101 378
gene59 89 827 138

How do I go about doing this?

Answer 1

[Guillaume]

Probably the easiest:

geneswithdata = readtable('data.txt');  %load file as a table
geneswithdata.Properties.VariableNames{1} = 'genes';  %rename first column for clarity (optional). 
%I would also rename all the other columns

genesonly = readtable('genelist.txt');  %load as a table
genesonly.Properties.VariableNames = {'genes'};  %rename columns. Common columns must have the same name

filteredgenes = innerjoin(genesonly, geneswithdata);

Done.

Using ismember that last line could be done as:

found = ismember(geneswithdata, genesonly);
filteredgenes = geneswithdata(found, :);

Using intersect (rather than setdiff) it could be done as:

[~, tokeep] = intersect(geneswithdata, genesonly);
filteredgenes = geneswithdata(tokeep, :);

[astein]

This almost got me there. The only issue is that I lose the first line/first gene of genelist.txt. This is an easy fix if I simply edit genelist.txt to:

genes
gene45
gene59
gene61

Is there another way I can prevent losing that first line if I'm loading files as tables?

Thank you!

[Guillaume]

By default, readtable considers the first line as a header line that is to be used to name the variables. To tell it to not do that:

readtable(___, 'ReadVariableNames', false)

readtable is extremely flexible. Look at its documentation to see all the options available.

[astein]

Thank you very much for the help!

Answer 2

[Image Analyst]

Look into ismember() or setdiff()

[astein]

I don't know how to use either for this purpose. setdiff() is going to give me the genes they don't have in common? I want the genes they have in common. ismember() gives me a logical array. I run into the same issue of how do I use the array to pull out only the rows that are "true". I am having difficulty manipulating the datasets (which format to load the txt files--structure, table, etc).