A commandline program to automatically identify markers predictive of groups. Can be used with binary data, genomic (single nucleotide variant) data, or arbitrary character data.
If you are on Windows and prefer a GUI, check out GenomeFisher
feht - predictive marker discovery
Usage: feht (-i|--infoFile FILE) (-d|--datafile FILE)
[--one "Group1Name Group1Item Group1Item Group1Item"]
[--two "Group2Name Group2Item Group2Item Group2Item"]
[-l|--delimiter [',', '\t' ...], DEFAULT='\t']
[-m|--mode ['binary', 'snp'], DEFAULT='binary']
[-c|--correction ['none', 'bonferroni'], DEFAULT='bonferroni']
[-f|--ratioFilter [Filter results by ratio (0.00-1.0), DEFAULT=0]]
Predictive marker discovery for groups; binary data, genomic data (single nucleotide variants), and arbitrary character data.
Available options:
-i,--infoFile FILE File of metadata information
-d,--datafile FILE File of binary or single-nucleotide variant data
--one "Group1Name Group1Item Group1Item Group1Item"
Group1 column name, followed by optional Group1
labels to include as part of the group
--two "Group2Name Group2Item Group2Item Group2Item"
Group2 column name, followed by optional Group2
labels to include as part of the group
-l,--delimiter [',', '\t' ...], DEFAULT='\t'
Delimiter used for both the metadata and data file
-m,--mode ['binary', 'snp'], DEFAULT='binary'
Mode for program data; either 'binary' or 'snp'
-c,--correction ['none', 'bonferroni'], DEFAULT='bonferroni'
Multiple-testing correction to apply
-f,--ratioFilter [Filter results by ratio (0.00-1.0), DEFAULT=0]
Display only those results greater than or equal to
the value
-h,--help Show this help text
feht is written in Haskell and is most easily built using the Haskell Tool Stack.
Taken from the Stack documentation above, Stack can be installed on a Unix-like system by running:
wget -qO- https://get.haskellstack.org/ | sh
Following the installation of Stack, feht can be built and tested by running in the project root directory:
stack test
All tests should pass, following which:
stack install
Will copy the compiled executable to your local bin/ path.
Compiled binaries of feht for Linux and Windows can be found here: binaries
Installation also possible from Bioconda
conda install -c bioconda feht
The program takes command line arguments, of which 2 are required: -i, which specifies the information (eg. metadata) file, and -d, which specifies the data file. Both of these files need to be delimited with the same delimiter, eg. tab (\t, which is the default).
The information file should be formatted with sample names in the first column, which does not require a header; sample names need to be identical in both the information and data files. All other columns require a header, and this header will be used as a metadata category; all subsequent rows will be interpreted as values within that category. For example, the data/test_metadata.txt file included in this repository is as follows:
genomes group position
GenomeA B up
GenomeB A up
GenomeC A down
GenomeD C sideways
GenomeE B down
GenomeF A down
GenomeG A floating
GenomeH A up
GenomeI B sideways
GenomeJ C down
GenomeK B up
The first column contains the sample names, GenomeA, GenomeB ... and though not required also contains a column header. Both group and postion will be interpreted as metadata categories, and A, B, C as values within metadata category group, and up, down, sideways, floating as values with metadata category position.
The corresponding data file data/test_binary.txt looks as follows:
GenomeA GenomeB GenomeC GenomeD GenomeE GenomeF GenomeG GenomeH GenomeI GenomeJ GenomeK GenomeL
binary1 0 - 0 0 1 0 0 1 0 0 1 1
binary2 0 0 0 0 0 0 0 0 0 0 0 0
binary3 1 1 0 0 0 0 1 1 1 1 0 0
binary4 1 0 0 1 1 0 0 - 0 0 1 0
... (truncated for space)
In the data file, the sample names are the column headers, and must exactly match those provided in the information (metadata) file. The first column in the data file lacks a column header, but contains labels for the data being examined, in this case snp1, snp2, snp3, snp4 .... Each row represents values of the data being examined for each sample.
feht by default will perform all possible pairwise comparisons given the categories in the information file. In our example using the data/test_metadata.txt file, a separate comparison within the group category of (A vs. B, A vs. C, A vs (B and C),B vs. C, B vs. (A and C), C vs. (A and B)) will be performed, and likewise within the position category. With our test data, these comparisons can be run with:
feht -i data/test_metadata.txt -d data/test_binary.txt
If you wish to save the results to a file, pipe them to the filename of your choice:
feht -i data/test_metadata.txt -d data/test_binary.txt > results.txt
And will produce an output file sorted from "most" to "least" discriminatory data. In our example that looks like:
[#-
Group1 category: group Group1: B
Group2 category: group Group2: C
---
Name GroupOne (+) GroupOne (-) GroupTwo (+) GroupTwo (-) pValue Ratio
binary21 4 0 0 2 1.0 1.0
binary44 3 1 0 2 1.0 0.75
binary42 3 1 0 2 1.0 0.75
binary24 1 3 1 0 1.0 -0.75
...
-#]
[#-
Group1 category: position Group1: sideways
Group2 category: position Group2: up
---
Name GroupOne (+) GroupOne (-) GroupTwo (+) GroupTwo (-) pValue Ratio
binary9 2 0 1 4 1.0 0.8
binary47 2 0 1 4 1.0 0.8
binary8 0 2 4 1 1.0 -0.8
binary49 2 0 1 4 1.0 0.8
binary1 0 2 3 1 1.0 -0.75
...
-#]
...
Each output block lists the categories that are being compared, and the values within the category that constitute the group. For example, the first output block above is a comparison between B and C within the group category. The output consists of seven columns, the first being the data label that was compared, and the next four showing the presence and absence of that particular datum among the two groups. In the first example above, for the datum binary21, GroupOne (which is B from the category group) contained four members that were positive for binary21 and 0 that were negative. For GroupTwo (which is C from the category group) there were no members that were positive for binary21 and two members that were negative.
The next column is the P-value, which shows by default the bonferroni corrected value. In this example, due to the small sample size and number of comparisons, the corrected value is not significant (eg. 1.0).
The final column contains the ratio of the fraction of GroupOne positive minus the fraction of GroupTwo positive. In our example for binary21 this is (4/4 - 0/2), which gives the result of 1.0. The ratio provides an additional method for identifying data that are skewed between the groups under comparison. A value of 1.0 means that all of GroupOne was positive for the datum and all of GroupTwo was negative; conversely a ratio of -1.0 means that all of GroupOne was negative, and all of GroupTwo was positive.
By default all pairwise comparisons will be computed, but user-specified groups can be given as well. In our example, if we only wanted to compare A and B in the group category, we could specify both GroupOne and GroupTwo as follows:
feht -i data/test_metadata.txt -d data/test_binary.txt --one "group A" --two "group B"
More than one value per category can be specified, as follows:
feht -i data/test_metadata.txt -d data/test_binary.txt --one "position up down" --two "position sideways floating"
Easily performing a one vs. all comparison is done by specifying only GroupOne, which will then be compared to a group comprised of all non-specified values of the same category. For example:
feht -i data/test_metadata.txt -d data/test_binary.txt --one "position up"
The above will construct GroupOne as up and GroupTwo as down sideways floating.
By default, feht will output every result for every comparison. If you wish to limit the number of results, the ratioFilter can be used, where only results with a ratio greater than or equal to the value will be displayed. For example, in the first block of results above, if we set the ratioFilter to 1.0 as in the following:
feht -i data/test_metadata.txt -d data/test_binary.txt -f 1
Only a single result is returned:
[#-
Group1 category: group Group1: B
Group2 category: group Group2: C
---
Name GroupOne (+) GroupOne (-) GroupTwo (+) GroupTwo (-) pValue Ratio
binary21 4 0 0 2 1.0 1.0
-#]
By default the tab character ('\t') is used as a delimiter, but any single character can be used. To use the comma character (',') enter it using the -l argument ("el"), and single-quotes around the delimiter:
feht -i data/test_metadata.txt -d data/test_binary.txt -l ','
If desired, the multiple-testing correction can be turned off by specifying "none" to the -c option. For example, to run a comparison with no correction:
feht -i data/test_metadata.txt -d data/test_binary.txt -c none
feht by default operated on a table of binary data, but comes with built-in support for single-nucleotide variant (SNV) data.
For each data entry, feht will convert the SNV into a binary comparison for all four nucleotides. Consider the provided data in data/test_snps.txt:
GenomeA GenomeB GenomeC GenomeD GenomeE GenomeF GenomeG GenomeH GenomeI GenomeJ GenomeK GenomeL
snp1 T - T T C A A C A A C C
snp2 A T T A A A T A A T A T
snp3 C G T T A A G C C C A A
snp4 C T A C G T T - A A C A
...
If the following comparison is run:
feht -i data/test_metadata.txt -d data/test_snps.txt -m snp
The following is produced:
[#-
Group1 category: group Group1: B
Group2 category: group Group2: C
---
Name GroupOne (+) GroupOne (-) GroupTwo (+) GroupTwo (-) pValue Ratio
snp32_a 0 4 2 0 1.0 -1.0
snp45_a 0 4 2 0 1.0 -1.0
snp41_t 0 4 2 0 1.0 -1.0
snp21_t 0 4 2 0 1.0 -1.0
...
This shows that the data for snp32 has been converted into binary, with the nucleotide under comparison appended. For snp32_a this represents all A characters in the data as positive, and all C, T, and G characters as negative. All four comparisons are carried out for each row of SNV data.
Within the binary mode, if data are not in 1 or 0 form, they will be ignored, and will not contribute to the calculations as either a positive or negative value; the total data for groups will be adjusted to accommodate the missing data. The same is true for snp mode data that is not A, C, T, G For example:
GenomeA GenomeB GenomeC GenomeD GenomeE GenomeF GenomeG GenomeH GenomeI GenomeJ GenomeK GenomeL
snp1 T - T T C A A C A A C C
Contains 12 possible entries, but the one for GenomeB is of the form -. This entry will be ignored, and only 11 data points will be used. This means that if GroupOne normally has 4 members and contains GenomeB, for the snp1 calculations, it will be as if it only contained 3 members.