compute_TLS: Computation of tertiary lymphoid structures signature (TLS)...
In olapuentesantana/easier: Estimate Systems Immune Response from RNA-seq data
compute_TLS R Documentation
Computation of tertiary lymphoid structures
signature (TLS) score
Description
Calculates TLS score using the geometric-mean of the
expression of its signature genes, as defined in
Cabrita et al., Nature, 2020.
Usage
compute_TLS(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
TLS score in a column.
References
Cabrita, R., Lauss, M., Sanna, A., Donia, M.,
Skaarup Larsen, M., Mitra, S., Johansson, I., Phung, B.,
Harbst, K., Vallon-Christersson, J., et al. (2020).
Tertiary lymphoid structures improve immunotherapy and
survival in melanoma. Nature 577, 561–565.
olapuentesantana/easier documentation built on Feb. 25, 2024, 3:39 p.m.
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| compute_TLS | R Documentation |
Computation of tertiary lymphoid structures signature (TLS) score
Description
Calculates TLS score using the geometric-mean of the expression of its signature genes, as defined in Cabrita et al., Nature, 2020.
Usage
compute_TLS(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 TLS score in a column.
References
Cabrita, R., Lauss, M., Sanna, A., Donia, M., Skaarup Larsen, M., Mitra, S., Johansson, I., Phung, B., Harbst, K., Vallon-Christersson, J., et al. (2020). Tertiary lymphoid structures improve immunotherapy and survival in melanoma. Nature 577, 561–565.
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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