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Operate on clonotype tables

JoinSamples

Joins several clonotype tables together to form a joint clonotype abundance table. Joint clonotype holds information on all clonotypes that match under a certain comparison criteria (e.g. identical CDR3nt and V segment), their samples of origin and corresponding abundances. At least two samples should be specified for this routine. For two sample case also consider using :ref:`OverlapPair` routine.

Attention!

This is the most memory-demanding routine, especially for a large number of samples.

Command line usage

$VDJTOOLS JoinSamples \
[options] [sample1.txt sample2.txt sample3.txt ... if -m is not specified] output_prefix

Parameters:

Shorthand Long name Argument Description
-m --metadata path Path to metadata file. See See :ref:`common_params`
-i --intersect-type string Sample intersection rule. Defaults to aa. See :ref:`common_params`
-x --times-detected integer Minimal number of samples in which a clonotype should be detected to get to the final output. Default = 2
-p --plot   Turns on plotting. See :ref:`common_params`
-c --compress   Compressed output for clonotype table. See :ref:`common_params`
-h --help   Display help message

Tabular output

Summary table suffixed join.[value of -i argument].summary.txt is created with the following columns.

Column Description
<first sample id > Indicator for the first sample, either 0 or 1
<second sample id > Indicator for the second sample
...  
clonotypes Number of clonotypes detected in all samples that have 1 indicator in a given row.

Joint clonotype abundance table file having join.[value of -i argument].table.txt suffix that contains joint clonotypes detected in at least -x samples. Table structure is described in the section below.

Joint clonotype abundance table structure

First columns have the same meaning as in :ref:`vdjtools_format` clonotype abundance table, they are computed as follows:

  • Normalized frequency is computed as geometric mean of clonotype frequencies that comprise a given joint clonotype in intersected samples. If clonotype is missing, its frequency is set to 1e-9.

    Note

    Joint clonotype is formed as a union of all clonotype variants in all samples that match under the specified -i rule.

  • Normalized count is calculated by scaling normalized frequencies so that the joint clonotypes with smallest frequency has a count of 1.

  • Clonotype signature (CDR3nt, CDR3aa, V, D and J) is taken from a representative clonotype.

    Note

    When several clonotype variants are present in samples that correspond to the same clonotype under -i rule (e.g. several Variable segment variants when -i nt is set), only the most abundant form is selected as a representative clonotype to final output.

Column Description
count Normalized clonotype count
freq Normalized clonotype frequency
cdr3nt Representative CDR3 nucleotide sequence
cdr3aa Representative CDR3 amino acid sequence
v Representative Variable segment
d Representative Diversity segment
j Representative Joining segment
peak Index of a time point at which given clonotype reaches its maximum frequency
occurrences Number of samples the joint clonotype was detected in
<sample name> Frequency of a joint clonotype at corresponding sample
...  

Graphical output

A Venn diagram can be found in a file having join.[value of -i argument].venn.pdf suffix. Note that if there are more than 5 samples, it will be constructed for the first 5 samples. Plotting is performed using VennDiagram R package.

_static/images/modules/join-venn.png

Overlap of clonotype sets. See Venn diagram wiki article for the description.


PoolSamples

Pools clonotypes from several samples together and merges clonotypes that that match under a certain comparison criteria (e.g. identical CDR3nt and V segment). Note that this routine can be used with a single sample to aggregate the sameple, e.g. by CDR3 amino acid sequence, in this case CDR3 nucleotide sequence, V and J segments will be taken from a representative clonotype variant with the highest frequency.

Command line usage

$VDJTOOLS PoolSamples \
[options] [sample1.txt sample2.txt sample3.txt ... if -m is not specified] output_prefix

Parameters:

Shorthand Long name Argument Description
-m --metadata path Path to metadata file. See :ref:`common_params`
-i --intersect-type string Sample intersection rule. Defaults to strict. See :ref:`common_params`
-p --plot   Turns on plotting. See :ref:`common_params`
-c --compress   Compressed output for clonotype table. See :ref:`common_params`
-h --help   Display help message

Tabular output

Summary table suffixed pool.[value of -i argument].summary.txt is created with the following columns.

Column Description
incidence.count Indicator for the first sample, either 0 or 1
read.count Total number of reads associated with a given pooled clonotype
convergence Total number of clonotype variants that match the pooled clonotype under -i rule.

Pooled clonotype abundance table file having pool.[value of -i argument].summary.txt. Table structure is described in the section below.

Pooled clonotype abundance table structure

First columns have the same meaning as in :ref:`vdjtools_format` clonotype abundance table, they are computed as follows:

  • Pooled count is computed as the total number of reads associated with clonotype variants that match under the specified -i rule.
  • Frequency is computed as pooled count divided by total number of reads in all samples.
  • Clonotype signature (CDR3nt, CDR3aa, V, D and J) is taken from a representative clonotype in the same way as described for :ref:`joint_table_structure`.
Column Description
count Pooled clonotype count
freq Pooled clonotype frequency
cdr3nt Representative CDR3 nucleotide sequence
cdr3aa Representative CDR3 amino acid sequence
v Representative Variable segment
d Representative Diversity segment
j Representative Joining segment
incidence Number of samples containing clonotype variants that comprise a given pooled clonotype
convergence Total number of clonotype variants that match the pooled clonotype under -i rule

Graphical output

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