LncMod (version 1.1)

tri.basic: Overview of Triplets' Expression

Description

Plot to show effector/target expression in a triplet (or triplets).

Usage

tri.basic(tri, M.exp, E.exp, T.exp, index = 1, N = 0.25)

Arguments

tri

a dataframe (or matrix) representing triplets to plot in which the first column is modulator id,the second is effector id and the third column is target id.The id style must be consistent with rownames of M.exp E.exp T.exp,respectively.

M.exp

a numeric dataframe (or matrix) representing modulator expression profile whose rownames is modulator id.

E.exp

a numeric dataframe (or matrix) representing effector expression profile whose rownames is effector id.

T.exp

a numeric dataframe (or matrix) representing target expression profile whose rownames is target id.

index

a numeric vector (default 1) specifying rowindex of triplets to plot.

N

a numeric (rangs from 0 to 0.5,default 0.25) specifying proportion,by which LOW/HIGH sample group are extracted from a sorted modulator expression samples.

Value

A dataframe whose rownames represent rowindex of triplets and columns represent 6 kinds of value of the plot (P_effector_target, P_effector, P_target, R_low, R_high, P_low, P_high).

• P_effector_target the significance of linear fitted lines;
• P_effector the significance of difference between effector expression in LOW/HIGH sample group.
• P_target the significance of difference between target expression in LOW/HIGH sample group.
• R_low the effector-target correlation in LOW sample group;
• R_high the effector-target correlation in HIGH sample group;
• P_low the significance of R_low;
• P_high the significance of R_high;

Details

Note:All the arguments without default value must be assigned.

For each triplet,the plot consists of 3 parts.

The left-top is a barplot showing expression of effector in LOW/HIGH sample group. The right-top is a scatter diagram with a linear fitted line using the function lm.The scatter diagram shows expression of target versus effector in LOW/HIGH sample group in which red is the HIGH while green is the LOW.The right-bottom is a barplot showing expression of target in LOW/HIGH sample group.

Examples

#One triplet
tri.basic(tri=datatests[["tri_bs"]],M.exp=datatests[["M_exp"]],
          E.exp=datatests[["E_exp"]],T.exp=datatests[["T_exp"]])
#Two triplets (or more)
tri.basic(tri=datatests[["tri_bs"]],M.exp=datatests[["M_exp"]],
          E.exp=datatests[["E_exp"]],T.exp=datatests[["T_exp"]],
		  index=c(1,2))