compute_CYT: Compute cytolytic activity (CYT) score
In olapuentesantana/easier: Estimate Systems Immune Response from RNA-seq data
compute_CYT R Documentation
Compute cytolytic activity (CYT) score
Description
Calculates the CYT score using the geometric mean of its
signature genes, as defined in Rooney et al., Cell, 2015.
Usage
compute_CYT(matches, RNA_tpm)
Arguments
matches
numeric vector indicating the index of signature
genes in RNA_tpm.
RNA_tpm
data.frame containing TPM values with HGNC symbols
in rows and samples in columns.
Value
A numeric matrix with samples in rows and CTY score
in a column.
References
Rooney, M.S., Shukla, S.A., Wu, C.J., Getz, G.,
and Hacohen, N. (2015). Molecular and genetic properties
of tumors associated with local immune cytolytic activity.
Cell 160, 48–61. https://doi.org/10.1016/j.cell.2014.12.033.
olapuentesantana/easier documentation built on Feb. 25, 2024, 3:39 p.m.
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| compute_CYT | R Documentation |
Compute cytolytic activity (CYT) score
Description
Calculates the CYT score using the geometric mean of its signature genes, as defined in Rooney et al., Cell, 2015.
Usage
compute_CYT(matches, RNA_tpm)
Arguments
matches |
numeric vector indicating the index of signature
genes in |
RNA_tpm |
data.frame containing TPM values with HGNC symbols in rows and samples in columns. |
Value
A numeric matrix with samples in rows and CTY score in a column.
References
Rooney, M.S., Shukla, S.A., Wu, C.J., Getz, G., and Hacohen, N. (2015). Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160, 48–61. https://doi.org/10.1016/j.cell.2014.12.033.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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