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scran_markers
Marker detection for single-cell data
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Buffers for score_markers_pairwise() and friends.
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#include <score_markers_pairwise.hpp>
Public Attributes | |
| std::vector< Stat_ * > | mean |
| std::vector< Stat_ * > | detected |
| Stat_ * | cohens_d = NULL |
| Stat_ * | auc = NULL |
| Stat_ * | delta_mean = NULL |
| Stat_ * | delta_detected = NULL |
Buffers for score_markers_pairwise() and friends.
| Stat_ | Floating-point type for the output statistics. |
Pointer to an array of length equal to \(GN^2\), where \(G\) is the number of genes and \(N\) is the number of groups. This is a 3-dimensional array to be filled with the AUC for the comparison between each pair of groups for each gene; see ScoreMarkersPairwiseBuffers::cohens_d for more details. (Unlike Cohen's d, all values are positive; so here, values above 0.5 represent upregulation in group \(j\) compared to \(k\).) Alternatively NULL, in which case the AUC is not stored.
| Stat_* scran_markers::ScoreMarkersPairwiseBuffers< Stat_ >::cohens_d = NULL |
Pointer to an array of length equal to \(GN^2\), where \(G\) is the number of genes and \(N\) is the number of groups. This is a 3-dimensional \(G \times N \times N\) array to be filled with the Cohen's D for the comparison between each pair of groups for each gene.
The first dimension is the slowest changing, is of length equal to the number of genes, and represents the gene. The second dimension is the second-fastest changing, is of length equal to the number of groups, and represents the first group. The third dimension is the fastest changing, is also of length equal to the number of groups, and represents the second group.
Thus, the entry \((i, j, k)\) (i.e., effects[i * N * N + j * N + k]) represents the effect size of gene \(i\) upon comparing group \(j\) against group \(k\). Positive values represent upregulation in group \(j\) compared to \(k\).
Alternatively NULL, in which case the Cohen's D is not stored.
| Stat_* scran_markers::ScoreMarkersPairwiseBuffers< Stat_ >::delta_detected = NULL |
Pointer to an array of length equal to \(GN^2\), where \(G\) is the number of genes and \(N\) is the number of groups. This is a 3-dimensional array to be filled with the difference in the detected proportions for the comparison between each pair of groups for each gene; see ScoreMarkersPairwiseBuffers::cohens_d for more details. Alternatively NULL, in which case the difference in detected proportions is not stored.
| Stat_* scran_markers::ScoreMarkersPairwiseBuffers< Stat_ >::delta_mean = NULL |
Pointer to an array of length equal to \(GN^2\), where \(G\) is the number of genes and \(N\) is the number of groups. This is a 3-dimensional array to be filled with the difference in means for the comparison between each pair of groups for each gene; see ScoreMarkersPairwiseBuffers::cohens_d for more details. Alternatively NULL, in which case the difference in means is not stored.
| std::vector<Stat_*> scran_markers::ScoreMarkersPairwiseBuffers< Stat_ >::detected |
Vector of length equal to the number of groups. Each pointer corresponds to a group and points to an array of length equal to the number of genes, to be filled with the proportion of cells with detected expression in that group.
| std::vector<Stat_*> scran_markers::ScoreMarkersPairwiseBuffers< Stat_ >::mean |
Vector of length equal to the number of groups. Each pointer corresponds to a group and points to an array of length equal to the number of genes, to be filled with the mean expression of each gene in that group.
1.9.8