Révision 7e2d37e1 doc/sphinx_doc/build/text/ref.txt
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position of their center. Adajacent nucleosomes are compared two by |
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two. Comparison is based on a log likelihood ratio score. The issue of |
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comparison is adjacents nucleosomes merge or separation. Finally the |
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function returns a list of clusters and all computed *lod_scores*.
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function returns a list of clusters and all computed *llr_scores*.
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Each cluster ows an attribute *wp* for "well positionned". This |
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attribute is set as *TRUE* if the cluster is composed of exactly one |
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nucleosomes of each sample. |
| ... | ... | |
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Usage |
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~~~~~ |
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aggregate_intra_strain_nucs(samples, lod_thres = 20, coord_max = 2e+07)
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aggregate_intra_strain_nucs(samples, llr_thres = 20, coord_max = 2e+07)
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Arguments |
| ... | ... | |
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marker=..., strain=..., roi=..., inputs=..., outputs=...)* with *roi = |
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list(name=..., begin=..., end=..., chr=..., genome=...)*. |
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"lod_thres"
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"llr_thres"
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Log likelihood ration threshold. |
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| ... | ... | |
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Value |
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~~~~~ |
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Returns a list of clusterized nucleosomes, and all computed lod
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Returns a list of clusterized nucleosomes, and all computed llr
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scores. |
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|
| ... | ... | |
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~~~~~ |
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align_inter_strain_nucs(replicates, wp_nucs_strain_ref1 = NULL, |
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wp_nucs_strain_ref2 = NULL, corr_thres = 0.5, lod_thres = 100,
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wp_nucs_strain_ref2 = NULL, corr_thres = 0.5, llr_thres = 100,
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config = NULL, ...) |
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|
| ... | ... | |
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Correlation threshold. |
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"lod_thres"
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"llr_thres"
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| 239 | 239 |
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LOD cut off. |
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|
| ... | ... | |
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Value |
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~~~~~ |
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Returns a list of clusterized nucleosomes, and all computed lod
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Returns a list of clusterized nucleosomes, and all computed llr
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| 256 | 256 |
scores. |
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|
| ... | ... | |
| 1272 | 1272 |
Description |
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~~~~~~~~~~~ |
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Compute the likelihood log of two set of value from two models Vs. a |
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unique model. |
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Compute the log likelihood ratio of two or more set of value. |
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| 1278 | 1277 |
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Usage |
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~~~~~ |
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lod_score_vecs(x, y)
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llr_score_nvecs(xs)
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| 1283 | 1282 |
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| 1284 | 1283 |
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Arguments |
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~~~~~~~~~ |
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"x" |
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First vector. |
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"y" |
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"xs" |
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| 1293 | 1288 |
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Second vector.
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list of vectors.
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| 1295 | 1290 |
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| 1296 | 1291 |
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Value |
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~~~~~ |
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Returns the likelihood ratio. |
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Returns the log likelihood ratio.
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| 1301 | 1296 |
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| 1302 | 1297 |
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| 1303 | 1298 |
Author(s) |
| ... | ... | |
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lines(min:max,dnorm(min:max,mean1,sd1)*card1,col=2) |
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lines(min:max,dnorm(min:max,mean2,sd2)*card2,col=3) |
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lines(min:max,dnorm(min:max,mean(c(x1,x2)),sd(c(x1,x2)))*card2,col=4) |
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lod_score_vecs(x1,x2)
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llr_score_nvecs(list(x1,x2))
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R: nm |
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| ... | ... | |
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+-----------------+-----------------------------------------------------+ |
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| Author: | Florent Chuffart | |
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+-----------------+-----------------------------------------------------+ |
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| Version: | 2.3.41 |
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| Version: | 2.3.42 |
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+-----------------+-----------------------------------------------------+ |
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| License: | CeCILL | |
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+-----------------+-----------------------------------------------------+ |
Formats disponibles : Unified diff