Description Usage Arguments Value Examples

This function allows you to identify genes with loss of expression

1 | ```
receptLoss(exprMatrNml, exprMatrTum, nSdBelow, minPropPerGroup)
``` |

`exprMatrNml` |
A matrix of expression values from normal tissue. Each row is a gene, and each column is a patient or sample. Genes should be in same order as exprMatrTum. |

`exprMatrTum` |
A matrix of expression values from tumor tissue. Each row is a gene, and each column is a patient or sample. Genes should be in same order as exprMatrNml. |

`nSdBelow` |
The number of SD below the mean of the adjacent normal tissue to set the boundary between tumor subgroups. |

`minPropPerGroup` |
A value between 0-1 that represents the minimum proportion of samples that should be present in each of the two subgroups (defined by the boundary set by nSdBelow) for a particular gene. |

a nx7 matrix, with n equaling the number of genes. The columns are as follows:

geneNm - the gene name

lowerBound - the lower bound, or the value 'nSdBelow' the mean of the normal tissue expression data.

propTumLessThBound - the proportion of tumor samples with expression levels less than 'lowerBound'

muAb - "mu above", the mean expression value of tumors greater than (ie above) the 'lowerBound'.

'muBl' - "mu below", the mean expression value of tumors less than (ie below) the 'lowerBound'.

'deltaMu' - the difference between 'muAb' and 'muBl'.

meetsMinPropPerGrp - a logical indicating whether the proportion of samples in each group is greater than that set by 'minPropPerGroup'.

1 2 3 4 5 6 7 8 9 | ```
exprMatrNml <- matrix(abs(rnorm(100, mean=2)), nrow=10)
exprMatrTum <- matrix(abs(rnorm(100)), nrow=10)
geneNames <- paste0(letters[seq_len(nrow(exprMatrNml))],
seq_len(nrow(exprMatrNml)))
rownames(exprMatrNml) <- rownames(exprMatrTum) <- geneNames
nSdBelow <- 2
minPropPerGroup <- .2
rl <- receptLoss(exprMatrNml, exprMatrTum, nSdBelow, minPropPerGroup)
head(rl)
``` |

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