Description Usage Arguments Details Value Author(s) Examples
Gene links with q-values of coexpression value pairs in either of two conditions higher than the cutoff are retained, while the coexpression values of other links are set to zero.
1 2 3 4 | qLinkfilter(exprs.1, exprs.2,
cutoff = 0.25,
r.method = c("pearson", "spearman")[1],
q.method = c("BH", "holm", "hochberg", "hommel", "bonferroni", "BY", "fdr")[1])
|
exprs.1 |
a data frame or matrix for condition A, with rows as variables (genes) and columns as samples. |
exprs.2 |
a data frame or matrix for condition B, with rows as variables (genes) and columns as samples. |
cutoff |
the cutoff of q-value; must be within [0,1]. |
r.method |
a character string indicating 'pearson' (default) or 'spearman' correlation coefficient will be computed. |
q.method |
a character string indicating adjust method of p-value, default is 'BH'. |
For each of the two conditions, the coexpression values are associated with the corresponding p-values (student T-test of the zero nature of a PCC), and these p-values are sorted and transformed to q-values (false discovery rates). Gene links with q-values of coexpression values in either of two conditions lower than the cutoff are reserved.
A list with two components of data frames, one for filtered data of condition A, the other for the counterpart of condition B.
Bao-hong Liu, Hui Yu, Jing Yang
1 2 3 4 5 | data(exprs)
qLinkfilter(exprs[1:100,1:16],exprs[1:100,17:63],
cutoff=0.25,
r.method='pearson',
q.method='BH')
|
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