Next: QTL Projection, Up: Meta Analysis
The first step of the QTL meta-analysis is to intergate all the input genetic marker maps into a single one called the consensus marker map.
Before performing the construction of the consensus map, it is important to evaluate how the input maps are connected together. For each linkage group, InfoMap displays some descriptive statistics about the marker maps and for each pair of mapping experiments the program looks for common marker sequences. A common marker sequence is a set of at least two common markers for which the order in the two linkage groups is consistent. The marker order is said to be consistent even if the sequence is completely inverted between the two linkage groups.
For example, in the above figure the number of common marker sequences is 2. The first one (in red) involved 2 markers (umc116, umc5b), which order is reversed between the two chromosome, and the second one (in blue) involved 3 markers (umc110, bnl16.06, umc168).
Option | Usage | Type | Explanation
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-m,--mapdir | required | string | The directory which contains the XML files.
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-o,--output | required | string | The output file name.
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-t,--mrkth | optional | integer | The threshold on the occurence of the markers.
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For example,
%java org.metaqtl.main.InfoMap -m xmldb -t 2 -o info.txt
gives information on the mapping experiments which XML files are included in the directory xmldb
by keeping only markers which are defined in at least 2 mapping experiments.
The output of InfoMap is a plain text file. For each linkage group, results are introduced by a '>CR' tag followed by the name of the linkage group as follows:
>CR 7 Connected=true # # Table of the chromosomes # 1 Ribaut 12 9.67 2 Lubberstedt 9 10.34 3 Moreau 9 15.23 4 Rebai 9 13.26 5 Mechin 9 8.78 # # Average number of marker per chrom m=9.60 # Average interval marker distance=11.45 # |
# # Table of the number of common markers # # Total number of marker M=37 # Prop of common markers p=0.1650793650793651 # Chrom Index 1 2 3 4 5 Total Ribaut 1 1.0 1.0 Lubberstedt 2 1.0 2.0 1.0 4.0 Moreau 3 1.0 5.0 2.0 8.0 Rebai 4 1.0 2.0 5.0 3.0 11.0 Mechin 5 1.0 2.0 3.0 6.0 |
# # Table of the number of common sequences # Chrom Index 1 2 3 4 5 Ribaut 1 Lubberstedt 2 1.0 Moreau 3 2.0 1.0 Rebai 4 1.0 2.0 1.0 Mechin 5 1.0 1.0 # # Table of proportion of marker involved in common sequences # The value can be negative depending on the frame of the # common sequences # Chrom Index 1 2 3 4 5 Ribaut 1 Lubberstedt 2 1.0 Moreau 3 0.2 1.0 Rebai 4 1.0 0.2 1.0 Mechin 5 1.0 1.0 |
ConsMap is dedicated to the construction of consensus marker map.
The method implemented in MetaQTL is based on a Weigthed Least Square (WLS) strategy. Contrary to iterative projection procedure, this method makes it possible to integrate all maps in a single step. It is also possible to fix a genetic map as reference.
Option | Usage | Type | Explanation
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-m,--mapdir | required | string | The directory which contains the XML files.
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-o,--outstem | required | string | The output file stem.
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-r,--refmap | optional | string | The XML file of the reference map.
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-t,--mrkthresh | optional | integer | The threshold on the occurence of the markers.
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-d,--dubfile | optional | string | The file containg a list of markers to ignore.
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--mrkdico | optional | string | The marker dictionary.
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For example,
%java org.metaqtl.main.ConsMap \ > -m xmldb -r xmldb/IBM.xml -o consmap |
The result of ConsMap consists in two files:
Identifier | Value
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CR | The name of the linkage group.
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NM | The number of distinct markers positioned on the consensus linkage group.
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GF | The goodness-of-fit of the consensus linkage group.
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PV | The p-value associated to the goodness-of-fit.
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DF | The number of degree of freedoms of the residual.
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SR | The standardized residuals: first comes the name of the mapping experiment followed by the value of the residual. These values are ordered according to the order of the marker intervals in the linkage group of the mapping experiment.
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CR 7 NM 37 GF 182.0738940381568 PV 1.0 DF 7 SR Lubberstedt 1.6308530669014496E-13 SR Lubberstedt -9.205700855506115E-14 SR Lubberstedt -3.401706740747478E-14 SR Lubberstedt -1.049889614734477E-13 SR Lubberstedt 1.2471027908772377E-13 SR Lubberstedt -2.9725343354129593E-13 SR Mechin -4.797069139413729E-15 SR Mechin 5.484351947823543E-14 SR Mechin 6.830428378396427E-15 SR Mechin 0.7995364207820779 SR Mechin 0.3047608429054208 SR Mechin -6.98290111003849E-14 SR Moreau 9.661620158868837E-15 SR Moreau 10.85507243048007 SR Moreau -2.1096760232982783 SR Moreau -0.002216097065843051 ... |