error when using segment function

I get these errors when running this snippet of code that references another script (script attached as a matlab file)

[filt_in, data_in_segs_corrected, segment_params]=segment_filt_v2(data_to_segment,[],[],params.genome_build);
params.segment_params=segment_params;

Warning: The data contains more columns (number of channels) than rows (number of samples). Check that the data is not transposed inadvertently.

> In ctrlMsgUtils.warning (line 25)

In segment (line 76)

In segment_filt_v2>seg_fun (line 145)

In segment_filt_v2 (line 101)

Unrecognized function or variable 'jmax'.

Error in segment (line 236)

hh=hist(:,jmax);

Error in segment_filt_v2>seg_fun (line 145)

thm=segment([data_in(idx+1:end),ones(length(data_in)-idx,1)],[0 1 1],R2);

Error in segment_filt_v2 (line 101)

data_in_segs_corrected{Chr}(in,c-4)=seg_fun(Data{Chr}(in,c), R2);

[Walter Roberson]

We do not know what parameters you passed into the function, and we do not have the files

Gap_hg19
C:/TIGER/Gap_hg38.mat
Mouse_Gap
/Users/ak2394/Amnon/Other_genomes/Drosophila_genome/dm6_Gap

so we cannot test the code.

[Emily]

My apologies!

TIGER_folder='C:\TIGER'; % ! change as appropriate

genome_build='hg38'; % hg19, hg38, mm10, dm6

read_length=100; % refers to the alignability filter file, not the actual lengths of the reads (read lengths should be same or longer than those used for alignability file). Default=100

win_size=10000;

params.genome_build=genome_build;

params.read_length=read_length;

params.win_size=win_size;

params.TIGER_folder=TIGER_folder;

[Walter Roberson]

We do not have data_to_segment

[Emily]

I had to subset this to be able to upload it, but it still gives the same error.

[Mathieu NOE]

with the provided code and files I have this error message :

Unrecognized function or variable 'last_autosome'.

Error in segment_filt_v2 (line 70)

s=cell2mat(Data(1:last_autosome(genome_build)));

Answer 1

[Gayathri]

Hi @Emily,

I spent some time looking into the code, and I was able to face the same error as mentioned in your query.

The error is happening because for a certain case the data that goes into the "segment" function is a scalar. And when we try to retrieve the "size" of a scalar we get it as follows

And the function expects number of rows to be greater than columns, hence you receive the error mentioned.

I had modified the "seg_fun" function to identify the cause of the issue as shown below. You can also troubleshoot the issue by placing breakpoints in the "disp" command.

function data_out=seg_fun(data_in,R2)

% segment data
[tr1,tr2]=size([data_in,ones(length(data_in),1)]);
if tr1<=tr2
    disp("error condition");
end
thm=segment([data_in,ones(length(data_in),1)],[0 1 1],R2); % function segment requires the System Identification Toolbox
thm=thm([1 1:end-1]); % correction: segment always results in a shift of 1 in the coordinates


% failed segmentation resulting in all NaNs: iteratively remove 5 data points at a time until resolved
nan=length(find(isnan(thm)));
iter=1;
while nan>length(thm)*0.9  % if most windows per region between gaps = NaN, remove additional 5 data points from beginning of region for each iteration
    idx=5*iter;
    % segment
    [tr1,tr2]=size(data_in(idx+1:end));
    if tr1<=tr2
        disp("error condition");
    end
    thm=segment([data_in(idx+1:end),ones(length(data_in)-idx,1)],[0 1 1],R2);
    thm=thm([1 1:end-1]); % correction: segment always results in a shift of 1 in the coordinates
    thm=[NaN(idx,1); thm]; % add NaNs in the beginning
    nan=length(find(isnan(thm))); % recount number of NaNs
    iter=iter+1;
end

Pleaserefer to the screenshot below to get a better understand the cause of the issue.

For resolving the issue please refrain from calling the "segment" function when the data input is not in the required format.

And I also noticed that the data might be taken in different orders. Initially I faced the error around "sample 19, Chromosome 11", and next as shown in the screenshot.

I hope this helps in resolving the query. Please feel free to reach out in case of any queries. Thanks!