R语言GEO数据挖掘:步骤三:进行基因差异分析

Python012

R语言GEO数据挖掘:步骤三:进行基因差异分析,第1张

用limma包,这里注意,limma包是对基因芯片表达矩阵的分析,不能对逆转录RNAseq表达矩阵进行分析(因为数据特征不同),RNAseq需要用另一种方法

解读此表

但是上面的用法做不到随心所欲的指定任意两组进行比较,所有还有下一种方法

处理好了分组信息,再自定义比较元素

自定义函数进行比较

热土和火山图都是傻瓜式的,只要的前面得出的deg数据(也就是基因差异表达数据)是正确的

你好:

geoXY(SoDA)

geoXY()所属R语言包:SoDA

Geodetic coordinates from latitude and longitude

大地坐标经度纬度

译者:生物统计家园网 机器人LoveR

描述----------Description----------

Given a set of points on the earth's surface, in latitude and longitude form, this function returns the corresponding coordinates in X (east-west) and Y (north-south) distances along the surface of the earth, from a specified origin.

给定一组地球表面上的点,在经度和纬度的形式,这个函数返回相应的坐标X(东 - 西)和Y(北 - 南)的距离,以及表面的地球,从指定的来源。

用法----------Usage----------

geoXY(latitude, longitude, lat0, lon0, unit = 1)

参数----------Arguments----------

参数:latitude, longitude

Pairs of latitude and longitude values for the points to be used.

对要使用的点的纬度和经度值。

参数:lat0, lon0

The two latitude, longitude defining the origin for the desired coordinates. By default, the southwest corner of the datathat is, the minimum values for the supplied latitude and longitude coordinates.

两个纬度,经度确定所需的坐标的原点。默认情况下,西南角的数据,也就是说,所提供的纬度和经度坐标的最小值。

参数:unit

The unit to be used for the coordinates, in meterse.g., unit=1000 causes the coordinates to be in kilometers.

要使用的单元的坐标,以米为单位,例如,unit=1000导致的坐标是在公里。

Details

详细信息----------Details----------

The coordinates returned are an alternative to projecting the points onto a plane or other surface. Unlike projections, there is no distortion or approximation involved, other than computational error in the algorithm for geodetic distances. The coordinates are in principle exact replications of the latitude and longitude, but expressed in distances along the corresponding horizontal and vertical geodesics. Essentially, the coordinates are rotated to a parallel of latitude and a north-south meridian through the origin, and distances returned along those lines to the latitude and longitude of the data points. For purposes of data visualization, the advantage is that the points are suitable for plotting as x, y values directly, regardless of the location, so long as the range of the latitude is not large compared to the surface of the earth.

返回的坐标投影到一个平面上或其他表面上的点的替代品。与预测不同的是,有不产生失真或近似涉及比大地测量距离的算法的计算误差,以及其他。坐标是在原则的纬度和经度的精确复制,但在沿着其对应的水平和垂直的测地线的距离表示。从本质上讲,在坐标旋转origin,并沿着这些线路返回到的数据点的纬度和经度的距离通过一个平行的纬度和南北子午线。的数据可视化的目的,其优点是,点适合绘图作为x, y值直接的位置无关,只要相比,在地球表面的纬度范围并不大。

The specific computation can be imagined as follows. For each pair of latitude and longitude in the data, the corresponding x coordinate is the distance from the origin to a point that has the same latitude as the origin and the same longitude as the data. The y coordinate is the distance from the origin to a point with the same longitude as the origin and the same latitude as the data. In each case the distance is distance on the surface of the earth, as computed by the algorithm in geoDist, with a sign given by the corresponding difference in latitude (for the y coordinate) or longitude (for the x coordinate).

具体计算如下可想而知。对于每一对经度和纬度的数据,对应的x坐标是从产地到一个点为原点的纬度和经度相同的数据具有相同的距离。的y坐标是从原点到同一经度的起源和同一纬度上的数据点的距离。在每一种情况下的距离是在地球表面上的距离,如由该算法计算在geoDist,给出了对应的差异(y坐标)的纬度或经度(x坐标的标志) 。

值----------Value----------

A two-column matrix of coordinates, with column names "X", "Y".

两列的矩阵坐标,列名"X", "Y"。