Description Usage Arguments Details Value Author(s) See Also Examples

Calculate a distance between all pairs of individuals for two gene expression data sets

1 2 |

`e1` |
Numeric matrix of gene expression data, as individuals x genes. The row and column names must contain individual and gene identifiers. |

`e2` |
(Optional) Like |

`d.method` |
Calculate inter-individual distance as RMS difference or as correlation. |

`labels` |
Two character strings, to use as labels for the two data matrices in subsequent output. |

`verbose` |
if TRUE, give verbose output. |

We calculate the pairwise distance between all individuals (rows) in
`e1`

and all individuals in `e2`

. This distance is either the RMS
difference (`d.method="rmsd"`

) or the correlation
(`d.method="cor"`

).

A matrix with `nrow(e1)`

rows and `nrow(e2)`

columns,
containing the distances. The individual IDs are in the row and column
names. The matrix is assigned class `"lineupdist"`

.

Karl W Broman, [email protected]

`pulldiag`

, `omitdiag`

,
`summary.lineupdist`

, `plot2dist`

,
`disteg`

, `corbetw2mat`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ```
# load the example data
data(expr1, expr2)
# find samples in common
id <- findCommonID(expr1, expr2)
# calculate correlations between cols of x and cols of y
thecor <- corbetw2mat(expr1[id$first,], expr2[id$second,])
# subset at genes with corr > 0.8 and scale values
expr1s <- expr1[,thecor > 0.8]/1000
expr2s <- expr2[,thecor > 0.8]/1000
# calculate distance (using "RMS difference" as a measure)
d1 <- distee(expr1s, expr2s, d.method="rmsd", labels=c("1","2"))
# calculate distance (using "correlation" as a measure...really similarity)
d2 <- distee(expr1s, expr2s, d.method="cor", labels=c("1", "2"))
# pull out the smallest 8 self-self correlations
sort(pulldiag(d2))[1:8]
# summary of results
summary(d1)
summary(d2)
# plot histograms of RMS distances
plot(d1)
# plot histograms of correlations
plot(d2)
# plot distances against one another
plot2dist(d1, d2)
``` |

kbroman/lineup documentation built on April 3, 2018, 8:59 a.m.

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