exp2cell: exp2cell

Description Usage Arguments Value References Examples

View source: R/exp2cell.R

Description

Function 'exp2cell' use gene expression profiles to quantify cell abundance matrix. 'exp2cell' provides three methods for estimating the relative infiltration abundance of different cell types in the tumor microenvironment (TME), which including xCell, ssGSEA estimated method proposed by Şenbabaoğlu et al. and CIBERSORT.

Usage

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exp2cell(
  exp,
  method = "xCell",
  perm = 100,
  QN = TRUE,
  kcdf = c("Gaussian", "Poisson", "none")
)

Arguments

exp

The gene expression data set. A matrix with row names as symbols and columns as samples. Gene expression profiles were used to quantify cell abundance matrix.

method

Method must be one of "xCell", "ssGSEA" and "CIBERSORT".

perm

No. permutations; set to >=100 to calculate p-values (default = 100)

QN

Quantile normalization of input mixture (default = TRUE)

kcdf

By default, kcdf="Gaussian" which is suitable when input expression values are continuous, such as microarray fluorescent units in logarithmic scale, RNA-seq log-CPMs, log-RPKMs or log-TPMs. When input expression values are integer counts, such as those derived from RNA-seq experiments, then this argument should be set to kcdf="Poisson".

Value

Cell abundance matrix.

References

1. Aaron, M, Newman, et al. Robust enumeration of cell subsets from tissue expression profiles.[J]. Nature Methods, 2015. 2. Aran D , Hu Z , Butte A J . xCell: digitally portraying the tissue cellular heterogeneity landscape[J]. Genome Biology, 2017, 18(1):220. 3. Senbabaoglu, Yasin, Gejman R S , Winer A G , et al. Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures[J]. Genome biology, 2016, 17(1).

Examples

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#get breast cancer gene expression profile.
exp.example<-GetExampleData("exp.example")

#perform the exp2cell method. Method must be one of "xCell","ssGSEA" and "CIBERSORT".
cellmatrix<-exp2cell(exp=exp.example,method="ssGSEA") #cell abundance matrix

SMDIC documentation built on Nov. 13, 2020, 5:06 p.m.